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

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

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


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

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

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


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

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

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

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

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


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


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


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

  Time building chain proxies: 0.88, per 1000 atoms: 0.40
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (71.604, 41.828, 66.343, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

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

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

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


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

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

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

  Time building chain proxies: 0.78, per 1000 atoms: 0.35
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (70.208, 45.321, 57.552, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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


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

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

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

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

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


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

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

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


  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

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

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


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


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

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.277, 57.558, 52.238, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

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

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

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

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

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

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 1.19 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: 375
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.10e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.03e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.76e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.58e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.42e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.53 -   106.27: 107
      106.27 -   112.01: 2529
      112.01 -   117.75: 459
      117.75 -   123.49: 822
      123.49 -   129.23: 162
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.42    4.18 1.00e+00 1.00e+00 1.74e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.79    3.81 1.00e+00 1.00e+00 1.45e+01
  angle model="   0" pdb=" C   THR A  82 "
        model="   0" pdb=" N   THR A  83 "
        model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  128.08   -6.38 1.80e+00 3.09e-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  116.14   -3.54 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CA  ASP A  44 "
        model="   0" pdb=" CB  ASP A  44 "
        model="   0" pdb=" CG  ASP A  44 "
      ideal   model   delta    sigma   weight residual
     112.60  116.09   -3.49 1.00e+00 1.00e+00 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 969
       17.13 -    34.26: 43
       34.26 -    51.38: 13
       51.38 -    68.51: 6
       68.51 -    85.64: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.24  -16.76     0      5.00e+00 4.00e-02 1.12e+01
  dihedral model="   0" pdb=" CA  HIS A  43 "
           model="   0" pdb=" C   HIS A  43 "
           model="   0" pdb=" N   ASP A  44 "
           model="   0" pdb=" CA  ASP A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.21   15.79     0      5.00e+00 4.00e-02 9.97e+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
    -180.00 -124.49  -55.51     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 72
       0.035 -    0.070: 30
       0.070 -    0.105: 36
       0.105 -    0.140: 29
      Time building chain proxies: 0.88, per 1000 atoms: 0.40
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.416, 59.042, 64.742, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
   0.140 -    0.175: 9
  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    2.34    0.17 2.00e-01 2.50e+01 7.63e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.14e-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 5.75e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.023 2.00e-02 2.50e+03   4.73e-02 2.24e+01
        model="   0" pdb=" CG  ASP A  36 "    0.082 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "    0.072 2.00e-02 2.50e+03   2.73e-02 2.24e+01
        model="   0" pdb=" CG  PHE A  15 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "    0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.054 2.00e-02 2.50e+03   2.30e-02 1.59e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.045 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 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.26 -     1.93: 28
        1.93 -     2.60: 2302
        2.60 -     3.27: 6823
        3.27 -     3.93: 8110
        3.93 -     4.60: 12170
  Nonbonded interactions: 29433
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB2 TYR A  81 "
            model="   0" pdb="HD13 LEU A  93 "
     model   vdw
     1.264 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.429 1.850
  nonbonded model="   0" pdb=" HD1 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.486 2.270
  nonbonded model="   0" pdb=" O   TYR A  81 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     1.565 2.620
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.601 1.850
  ... (remaining 29428 not shown)

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

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

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

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

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

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

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: 0.84
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.98 seconds

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

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

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 10
        1.23 -     1.42: 461
        1.42 -     1.62: 661
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.306  0.024 1.30e-02 5.92e+03 3.33e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.339 -0.018 1.00e-02 1.00e+04 3.26e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.337 -0.016 1.00e-02 1.00e+04 2.48e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.337 -0.016 1.00e-02 1.00e+04 2.47e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.311  0.019 1.30e-02 5.92e+03 2.23e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.88 -   105.92: 45
      105.92 -   111.96: 2642
      111.96 -   118.00: 451
      118.00 -   124.04: 876
      124.04 -   130.08: 65
  Bond angle restraints: 4079
  Sorted by residual:
  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  125.61   -3.91 1.80e+00 3.09e-01 4.71e+00
  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  120.48    2.12 1.00e+00 1.00e+00 4.51e+00
  angle model="   0" pdb=" CB  GLU A  75 "
        model="   0" pdb=" CG  GLU A  75 "
        model="   0" pdb=" CD  GLU A  75 "
      ideal   model   delta    sigma   weight residual
     112.60  109.01    3.59 1.70e+00 3.46e-01 4.47e+00
  angle model="   0" pdb=" CA  ILE A  51 "
        model="   0" pdb=" C   ILE A  51 "
        model="   0" pdb=" N   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     116.90  119.86   -2.96 1.50e+00 4.44e-01 3.89e+00
  angle model="   0" pdb=" CB  HIS A 139 "
        model="   0" pdb=" CG  HIS A 139 "
        model="   0" pdb=" CD2 HIS A 139 "
      ideal   model   delta    sigma   weight residual
     131.20  128.88    2.32 1.30e+00 5.92e-01 3.20e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 973
       17.47 -    34.93: 34
       34.93 -    52.40: 13
       52.40 -    69.86: 4
       69.86 -    87.33: 9
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.54   20.46     0      5.00e+00 4.00e-02 1.67e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.33  -87.33     1      3.00e+01 1.11e-03 1.02e+01
  dihedral model="   0" pdb=" CB  GLU A  75 "
           model="   0" pdb=" CG  GLU A  75 "
           model="   0" pdb=" CD  GLU A  75 "
           model="   0" pdb=" OE1 GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.12   85.12     1      3.00e+01 1.11e-03 9.76e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 81
       0.030 -    0.060: 51
       0.060 -    0.090: 29
       0.090 -    0.120: 11
       0.120 -    0.149: 4
  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    2.66   -0.15 2.00e-01 2.50e+01 5.59e-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 4.01e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.82e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.029 2.00e-02 2.50e+03   1.15e-02 3.98e+00
        model="   0" pdb=" CG  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  45 "   -0.020 2.00e-02 2.50e+03   7.96e-03 1.90e+00
        model="   0" pdb=" CG  PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  45 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  45 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  45 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  45 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  45 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  45 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  45 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  45 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  45 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  45 "   -0.010 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLU A  75 "   -0.006 2.00e-02 2.50e+03   1.22e-02 1.50e+00
        model="   0" pdb=" CD  GLU A  75 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLU A  75 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OE2 GLU A  75 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     1.99: 26
        1.99 -     2.64: 2709
        2.64 -     3.29: 6523
        3.29 -     3.95: 7430
        3.95 -     4.60: 11414
  Nonbonded interactions: 28102
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HZ2 LYS A 125 "
     model   vdw
     1.334 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.572 1.850
  nonbonded model="   0" pdb=" O   GLU A 133 "
            model="   0" pdb=" HD2 HIS A 137 "
     model   vdw
     1.618 2.450
  nonbonded model="   0" pdb=" HB2 SER A  46 "
            model="   0" pdb=" HD3 LYS A 125 "
     model   vdw
     1.737 2.440
  nonbonded model="   0" pdb="HG12 ILE A  38 "
            model="   0" pdb=" HA  ASP A  44 "
     model   vdw
     1.799 2.440
  ... (remaining 28097 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

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

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


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

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

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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 0.86, per 1000 atoms: 0.39
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.92, 61.756, 41.362, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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


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

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

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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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

  Time building chain proxies: 0.99, per 1000 atoms: 0.45
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.782, 56.767, 57.709, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.577, 49.243, 56.709, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.65
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.74 seconds

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


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

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

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

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

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 668
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ILE A  86 "
       model="   0" pdb=" N   GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.32e+00
  bond model="   0" pdb=" C   VAL A 126 "
       model="   0" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.93e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.335 -0.014 1.00e-02 1.00e+04 1.88e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.308  0.013 1.00e-02 1.00e+04 1.74e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.42e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.47 -   106.61: 56
      106.61 -   112.76: 2711
      112.76 -   118.91: 439
      118.91 -   125.05: 831
      125.05 -   131.20: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CG  ARG A 129 "
        model="   0" pdb=" CD  ARG A 129 "
        model="   0" pdb=" NE  ARG A 129 "
      ideal   model   delta    sigma   weight residual
     112.00  115.80   -3.80 2.20e+00 2.07e-01 2.98e+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  104.06    4.94 3.00e+00 1.11e-01 2.72e+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  113.94   -4.94 3.00e+00 1.11e-01 2.71e+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  104.11    4.89 3.00e+00 1.11e-01 2.66e+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 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 986
       16.44 -    32.88: 28
       32.88 -    49.32: 12
       49.32 -    65.77: 4
       65.77 -    82.21: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" CB  GLU A  84 "
           model="   0" pdb=" CG  GLU A  84 "
           model="   0" pdb=" CD  GLU A  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.16   57.84     3      1.50e+01 4.44e-03 9.45e+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
     -60.00   -3.46  -56.54     3      1.50e+01 4.44e-03 9.40e+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  -75.61   75.61     1      3.00e+01 1.11e-03 8.02e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 97
       0.028 -    0.056: 57
       0.056 -    0.084: 11
       0.084 -    0.111: 7
       0.111 -    0.139: 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   -0.14 2.00e-01 2.50e+01 4.85e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.37e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.016 5.00e-02 4.00e+02   2.48e-02 9.85e-01
        model="   0" pdb=" N   PRO A   6 "   -0.043 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.008 2.00e-02 2.50e+03   4.34e-03 5.65e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.010 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 "   -0.000 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 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  GLY A  87 "    0.003 2.00e-02 2.50e+03   6.71e-03 4.51e-01
        model="   0" pdb=" C   GLY A  87 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" O   GLY A  87 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" N   ASP A  88 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.26: 264
        2.26 -     2.85: 5118
        2.85 -     3.43: 5457
        3.43 -     4.02: 7401
        4.02 -     4.60: 11194
  Nonbonded interactions: 29434
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   GLU A  84 "
            model="   0" pdb=" HG  SER A  90 "
     model   vdw
     1.680 1.850
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" HB2 ASP A  44 "
     model   vdw
     1.742 2.440
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" HD1 TYR A  91 "
     model   vdw
     1.781 2.270
  nonbonded model="   0" pdb=" HG2 GLU A  32 "
            model="   0" pdb="HH12 ARG A 129 "
     model   vdw
     1.786 2.270
  nonbonded model="   0" pdb=" HB3 LEU A   3 "
            model="   0" pdb="HD11 LEU A  53 "
     model   vdw
     1.799 2.440
  ... (remaining 29429 not shown)

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

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

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

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

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

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


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

  Time building chain proxies: 0.66, per 1000 atoms: 0.30
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.809, 57.725, 56.551, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 115
        1.23 -     1.43: 358
        1.43 -     1.63: 659
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" N   PRO A 102 "
       model="   0" pdb=" CD  PRO A 102 "
    ideal  model  delta    sigma   weight residual
    1.473  1.428  0.045 1.40e-02 5.10e+03 1.02e+01
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.40e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.02e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.97e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.41e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.76 -   105.65: 62
      105.65 -   111.54: 2444
      111.54 -   117.43: 557
      117.43 -   123.31: 839
      123.31 -   129.20: 177
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.46    4.14 1.00e+00 1.00e+00 1.72e+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  118.92    3.68 1.00e+00 1.00e+00 1.35e+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  116.08   -3.48 1.00e+00 1.00e+00 1.21e+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  127.89   -6.19 1.80e+00 3.09e-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  129.20   -4.80 1.40e+00 5.10e-01 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 961
       17.33 -    34.66: 50
       34.66 -    51.99: 15
       51.99 -    69.32: 6
       69.32 -    86.65: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.47   19.53     0      5.00e+00 4.00e-02 1.53e+01
  dihedral model="   0" pdb=" CA  PRO A 102 "
           model="   0" pdb=" C   PRO A 102 "
           model="   0" pdb=" N   ASP A 103 "
           model="   0" pdb=" CA  ASP A 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.84   16.16     0      5.00e+00 4.00e-02 1.04e+01
  dihedral model="   0" pdb=" N   HIS A 134 "
           model="   0" pdb=" CA  HIS A 134 "
           model="   0" pdb=" CB  HIS A 134 "
           model="   0" pdb=" CG  HIS A 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.62  -54.38     3      1.50e+01 4.44e-03 9.28e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 74
       0.042 -    0.083: 45
       0.083 -    0.125: 35
       0.125 -    0.166: 19
       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  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 9.61e-01
  chirality model="   0" pdb=" CG  LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
            model="   0" pdb=" CD1 LEU A  93 "
            model="   0" pdb=" CD2 LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.35e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "   -0.256 2.00e-02 2.50e+03   1.03e-01 3.20e+02
        model="   0" pdb=" CG  PHE A  15 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "    0.062 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "    0.113 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "    0.116 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "   -0.151 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.221 2.00e-02 2.50e+03   1.01e-01 3.03e+02
        model="   0" pdb=" CG  TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.209 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.085 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.083 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.065 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.120 2.00e-02 2.50e+03   4.95e-02 7.34e+01
        model="   0" pdb=" CG  TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.088 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 91
        2.12 -     2.74: 3878
        2.74 -     3.36: 6204
        3.36 -     3.98: 7499
        3.98 -     4.60: 11357
  Nonbonded interactions: 29029
  Sorted by model distance:
  nonbonded model="   0" pdb="HG13 ILE A  86 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.501 2.270
  nonbonded model="   0" pdb=" HE2 TYR A  89 "
            model="   0" pdb=" HD3 PRO A 102 "
     model   vdw
     1.599 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.667 1.850
  nonbonded model="   0" pdb=" HE2 PHE A  15 "
            model="   0" pdb="HG23 ILE A  86 "
     model   vdw
     1.725 2.270
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.784 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, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.5, 74.988, 60.943, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 0.97, per 1000 atoms: 0.44
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.807, 35.635, 71.719, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

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

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

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

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


  Symmetric amino acids flipped
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

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

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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (78.052, 43.649, 48.561, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Time building chain proxies: 1.22, per 1000 atoms: 0.55
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.604, 70.183, 55.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

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

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


  Symmetric amino acids flipped
    Residue "A GLU   49": "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"
  Time to flip residues: 0.00s

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

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

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

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

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

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

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (75.312, 39.356, 50.849, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.80 seconds

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

  Time building chain proxies: 0.74, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.912, 52.923, 53.201, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.79 seconds

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 110
        1.23 -     1.43: 362
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 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 9.05e+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 7.10e+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 7.00e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.48e+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 6.20e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.16 -   105.89: 86
      105.89 -   111.63: 2438
      111.63 -   117.36: 532
      117.36 -   123.09: 797
      123.09 -   128.82: 226
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.47    4.13 1.00e+00 1.00e+00 1.71e+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  126.51    4.69 1.30e+00 5.92e-01 1.30e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.10   -3.50 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.12    3.48 1.00e+00 1.00e+00 1.21e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  115.83   -3.23 1.00e+00 1.00e+00 1.04e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 957
       17.23 -    34.45: 54
       34.45 -    51.68: 16
       51.68 -    68.91: 5
       68.91 -    86.13: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.81   27.19     0      5.00e+00 4.00e-02 2.96e+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  156.96   23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.06   21.94     0      5.00e+00 4.00e-02 1.92e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.041: 68
       0.041 -    0.081: 49
       0.081 -    0.120: 36
       0.120 -    0.160: 17
       0.160 -    0.200: 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    2.31    0.20 2.00e-01 2.50e+01 9.98e-01
  chirality model="   0" pdb=" CA  SER A  98 "
            model="   0" pdb=" N   SER A  98 "
            model="   0" pdb=" C   SER A  98 "
            model="   0" pdb=" CB  SER A  98 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 7.81e-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 7.20e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.213 2.00e-02 2.50e+03   9.77e-02 2.86e+02
        model="   0" pdb=" CG  TYR A  81 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.043 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 "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.204 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.078 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.085 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.057 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.080 2.00e-02 2.50e+03   3.49e-02 3.65e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.070 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.056 2.00e-02 2.50e+03   2.16e-02 1.40e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 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 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 87
        2.12 -     2.74: 3824
        2.74 -     3.36: 6119
        3.36 -     3.98: 7335
        3.98 -     4.60: 10969
  Nonbonded interactions: 28334
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.503 1.850
  nonbonded model="   0" pdb=" OH  TYR A  81 "
            model="   0" pdb=" HG  SER A  98 "
     model   vdw
     1.522 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.758 1.850
  nonbonded model="   0" pdb="HD11 LEU A  64 "
            model="   0" pdb=" HE3 LYS A 101 "
     model   vdw
     1.783 2.440
  ... (remaining 28329 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (69.147, 49.352, 50.903, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 62
        1.23 -     1.42: 410
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.13e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.33e+00
  bond model="   0" pdb=" C   THR A  92 "
       model="   0" pdb=" N   LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.367 -0.038 1.40e-02 5.10e+03 7.28e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 7.01e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.32e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.15 -   105.89: 88
      105.89 -   111.64: 2438
      111.64 -   117.38: 531
      117.38 -   123.13: 805
      123.13 -   128.87: 217
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.38    4.22 1.00e+00 1.00e+00 1.78e+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  115.24    6.46 1.80e+00 3.09e-01 1.29e+01
  angle model="   0" pdb=" C   GLY A  87 "
        model="   0" pdb=" N   ASP A  88 "
        model="   0" pdb=" CA  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     121.70  128.02   -6.32 1.80e+00 3.09e-01 1.23e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.74    4.46 1.30e+00 5.92e-01 1.18e+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  119.19    3.41 1.00e+00 1.00e+00 1.16e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 956
       17.05 -    34.09: 57
       34.09 -    51.14: 16
       51.14 -    68.19: 3
       68.19 -    85.23: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.56   44.44     0      5.00e+00 4.00e-02 7.90e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.60   38.40     0      5.00e+00 4.00e-02 5.90e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.78   30.22     0      5.00e+00 4.00e-02 3.65e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 78
       0.047 -    0.093: 49
       0.093 -    0.139: 39
       0.139 -    0.185: 8
       0.185 -    0.231: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.66e-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    2.33    0.18 2.00e-01 2.50e+01 8.25e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.073 2.00e-02 2.50e+03   3.05e-02 2.80e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.026 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 "   -0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.050 2.00e-02 2.50e+03   1.96e-02 1.16e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  LEU A  93 "    0.016 2.00e-02 2.50e+03   3.25e-02 1.06e+01
        model="   0" pdb=" C   LEU A  93 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" O   LEU A  93 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" N   GLY A  94 "    0.019 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 368
        2.30 -     2.88: 5159
        2.88 -     3.45: 5352
        3.45 -     4.03: 7023
        4.03 -     4.60: 10446
  Nonbonded interactions: 28348
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.730 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.763 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.836 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.844 1.850
  ... (remaining 28343 not shown)

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

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

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

  Time building geometry restraints manager: 1.20 seconds

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

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.048, 59.213, 43.315, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 125
        1.23 -     1.43: 347
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.04e+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 7.86e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.66e+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 6.95e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.33e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.72 -   106.32: 119
      106.32 -   111.93: 2491
      111.93 -   117.53: 460
      117.53 -   123.13: 792
      123.13 -   128.74: 217
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.80    3.80 1.00e+00 1.00e+00 1.45e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.95    3.65 1.00e+00 1.00e+00 1.33e+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  119.01    3.59 1.00e+00 1.00e+00 1.29e+01
  angle model="   0" pdb=" CA  GLY A 121 "
        model="   0" pdb=" C   GLY A 121 "
        model="   0" pdb=" N   ILE A 122 "
      ideal   model   delta    sigma   weight residual
     116.20  123.06   -6.86 2.00e+00 2.50e-01 1.18e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.78    4.42 1.30e+00 5.92e-01 1.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.42: 963
       16.42 -    32.84: 45
       32.84 -    49.26: 19
       49.26 -    65.68: 3
       65.68 -    82.10: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.37   33.63     0      5.00e+00 4.00e-02 4.52e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.99   19.01     0      5.00e+00 4.00e-02 1.45e+01
  dihedral model="   0" pdb=" CA  VAL A 112 "
           model="   0" pdb=" C   VAL A 112 "
           model="   0" pdb=" N   LYS A 113 "
           model="   0" pdb=" CA  LYS A 113 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.14   17.86     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 1030 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  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  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 9.81e-01
  chirality model="   0" pdb=" CA  LEU A 119 "
            model="   0" pdb=" N   LEU A 119 "
            model="   0" pdb=" C   LEU A 119 "
            model="   0" pdb=" CB  LEU A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.66e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.060 2.00e-02 2.50e+03   2.60e-02 2.03e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 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 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.051 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 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.063 2.00e-02 2.50e+03   2.45e-02 1.81e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.044 2.00e-02 2.50e+03   1.69e-02 8.54e+00
        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 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 151
        2.18 -     2.78: 4257
        2.78 -     3.39: 6162
        3.39 -     3.99: 7568
        3.99 -     4.60: 11297
  Nonbonded interactions: 29435
  Sorted by model distance:
  nonbonded model="   0" pdb="HD22 LEU A 119 "
            model="   0" pdb="HD12 ILE A 122 "
     model   vdw
     1.569 2.440
  nonbonded model="   0" pdb="HD22 LEU A 119 "
            model="   0" pdb="HG13 ILE A 122 "
     model   vdw
     1.591 2.440
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.712 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.721 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.739 1.850
  ... (remaining 29430 not shown)

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

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.27 seconds

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

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

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 79
        1.23 -     1.43: 393
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.78e+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 6.96e+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 6.04e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.90e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.81e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.00 -   105.81: 74
      105.81 -   111.62: 2452
      111.62 -   117.43: 538
      117.43 -   123.23: 828
      123.23 -   129.04: 187
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.42    4.18 1.00e+00 1.00e+00 1.74e+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  116.20   -3.60 1.00e+00 1.00e+00 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  119.05    3.55 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.84    4.36 1.30e+00 5.92e-01 1.13e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.04   -4.64 1.40e+00 5.10e-01 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 968
       17.54 -    35.07: 44
       35.07 -    52.61: 16
       52.61 -    70.15: 3
       70.15 -    87.69: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.44   21.56     0      5.00e+00 4.00e-02 1.86e+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  159.58   20.42     0      5.00e+00 4.00e-02 1.67e+01
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.28  -18.72     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 69
       0.044 -    0.088: 49
       0.088 -    0.131: 39
       0.131 -    0.175: 16
       0.175 -    0.219: 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    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality model="   0" pdb=" CB  THR A  83 "
            model="   0" pdb=" CA  THR A  83 "
            model="   0" pdb=" OG1 THR A  83 "
            model="   0" pdb=" CG2 THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.40e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.066 2.00e-02 2.50e+03   2.84e-02 2.41e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 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 "   -0.006 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 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.023 2.00e-02 2.50e+03   4.72e-02 2.23e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.082 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.028 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 1.75e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.44 -     2.07: 58
        2.07 -     2.70: 3429
        2.70 -     3.34: 6335
        3.34 -     3.97: 7515
        3.97 -     4.60: 11347
  Nonbonded interactions: 28684
  Sorted by model distance:
  nonbonded model="   0" pdb="HG21 THR A  83 "
            model="   0" pdb=" HA  THR A  92 "
     model   vdw
     1.440 2.440
  nonbonded model="   0" pdb="HG23 THR A  83 "
            model="   0" pdb=" H   LEU A  93 "
     model   vdw
     1.452 2.270
  nonbonded model="   0" pdb="HG23 THR A  83 "
            model="   0" pdb=" HA  THR A  92 "
     model   vdw
     1.556 2.440
  nonbonded model="   0" pdb=" HA  THR A  83 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     1.606 2.440
  nonbonded model="   0" pdb=" H   THR A  83 "
            model="   0" pdb=" O   LEU A  93 "
     model   vdw
     1.640 1.850
  ... (remaining 28679 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.613, 46.794, 43.544, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  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.

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

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

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

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

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

  Time building geometry restraints manager: 1.20 seconds

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


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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 87
        1.23 -     1.43: 385
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.93e+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 6.29e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.80e+00
  bond model="   0" pdb=" CZ  ARG A 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 5.62e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.42e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   106.17: 103
      106.17 -   111.80: 2484
      111.80 -   117.43: 481
      117.43 -   123.06: 783
      123.06 -   128.69: 228
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.75   -4.15 1.00e+00 1.00e+00 1.72e+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  118.61    3.99 1.00e+00 1.00e+00 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  126.29    4.91 1.30e+00 5.92e-01 1.43e+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 1.33e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.10   -3.50 1.00e+00 1.00e+00 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.47: 926
       13.47 -    26.95: 74
       26.95 -    40.42: 20
       40.42 -    53.90: 8
       53.90 -    67.37: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.39  -23.61     0      5.00e+00 4.00e-02 2.23e+01
  dihedral model="   0" pdb=" N   ASP A  95 "
           model="   0" pdb=" CA  ASP A  95 "
           model="   0" pdb=" CB  ASP A  95 "
           model="   0" pdb=" CG  ASP A  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.28  -59.72     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   0" pdb=" N   HIS A 134 "
           model="   0" pdb=" CA  HIS A 134 "
           model="   0" pdb=" CB  HIS A 134 "
           model="   0" pdb=" CG  HIS A 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.19  -58.81     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 74
       0.042 -    0.084: 48
       0.084 -    0.126: 36
       0.126 -    0.168: 14
       0.168 -    0.210: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.59e-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 7.87e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.209 2.00e-02 2.50e+03   8.33e-02 2.08e+02
        model="   0" pdb=" CG  TYR A  81 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.144 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.077 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.025 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.124 2.00e-02 2.50e+03   5.20e-02 8.10e+01
        model="   0" pdb=" CG  TYR A  89 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.098 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "   -0.119 2.00e-02 2.50e+03   4.87e-02 7.11e+01
        model="   0" pdb=" CG  PHE A  15 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "    0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "   -0.070 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.44 -     2.07: 69
        2.07 -     2.70: 3511
        2.70 -     3.34: 6394
        3.34 -     3.97: 7673
        3.97 -     4.60: 11671
  Nonbonded interactions: 29318
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   THR A  82 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     1.438 2.620
  nonbonded model="   0" pdb=" HD2 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.473 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.593 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.596 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.704 1.850
  ... (remaining 29313 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.907, 45.455, 82.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.94 seconds

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


  Symmetric amino acids flipped
    Residue "A GLU   75": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 1
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 137 "
       model="   0" pdb=" N   HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.329  1.303  0.026 1.40e-02 5.10e+03 3.38e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.18e+00
  bond model="   0" pdb=" C   THR A  82 "
       model="   0" pdb=" N   THR A  83 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.40e-02 5.10e+03 2.07e+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 1.77e+00
  bond model="   0" pdb=" C   GLU A  75 "
       model="   0" pdb=" N   SER A  76 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.59e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.64 -   106.72: 55
      106.72 -   112.79: 2706
      112.79 -   118.87: 442
      118.87 -   124.95: 834
      124.95 -   131.02: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.21   -5.21 3.00e+00 1.11e-01 3.01e+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  103.98    5.02 3.00e+00 1.11e-01 2.80e+00
  angle model="   0" pdb=" C   PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  104.10    4.90 3.00e+00 1.11e-01 2.67e+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  104.15    4.85 3.00e+00 1.11e-01 2.61e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.58   -4.58 3.00e+00 1.11e-01 2.33e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 979
       17.27 -    34.54: 33
       34.54 -    51.81: 12
       51.81 -    69.08: 3
       69.08 -    86.35: 6
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.35   86.35     1      3.00e+01 1.11e-03 9.99e+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  -78.16   78.16     1      3.00e+01 1.11e-03 8.48e+00
  dihedral model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
           model="   0" pdb=" CD  GLU A  55 "
           model="   0" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   73.00  -73.00     1      3.00e+01 1.11e-03 7.55e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 108
       0.027 -    0.054: 47
       0.054 -    0.081: 10
       0.081 -    0.108: 7
       0.108 -    0.135: 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    2.57   -0.14 2.00e-01 2.50e+01 4.58e-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   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.64e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.019 2.00e-02 2.50e+03   7.31e-03 1.60e+00
        model="   0" pdb=" CG  TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.015 5.00e-02 4.00e+02   2.27e-02 8.23e-01
        model="   0" pdb=" N   PRO A   6 "   -0.039 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.013 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.007 2.00e-02 2.50e+03   4.35e-03 5.68e-01
        model="   0" pdb=" CG  TYR A  81 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 164
        2.20 -     2.80: 4591
        2.80 -     3.40: 5842
        3.40 -     4.00: 7410
        4.00 -     4.60: 11191
  Nonbonded interactions: 29198
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 LEU A  70 "
            model="   0" pdb="HD11 ILE A  78 "
     model   vdw
     1.599 2.440
  nonbonded model="   0" pdb="HG21 ILE A  78 "
            model="   0" pdb=" HB2 LEU A  99 "
     model   vdw
     1.675 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.689 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" O   LYS A  79 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.754 1.850
  ... (remaining 29193 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.71, per 1000 atoms: 0.32
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (72.032, 60.139, 40.749, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  80 "
       model="   0" pdb=" N   TYR A  81 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.28e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.11e+00
  bond model="   0" pdb=" C   HIS A 135 "
       model="   0" pdb=" N   HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.73e+00
  bond model="   0" pdb=" CD2 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.386 -0.012 1.10e-02 8.26e+03 1.26e+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 1.11e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.22 -   106.38: 46
      106.38 -   112.54: 2712
      112.54 -   118.70: 444
      118.70 -   124.86: 834
      124.86 -   131.02: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.87    5.13 3.00e+00 1.11e-01 2.92e+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  113.97   -4.97 3.00e+00 1.11e-01 2.74e+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  104.17    4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.48   -4.48 3.00e+00 1.11e-01 2.23e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.32   -4.32 3.00e+00 1.11e-01 2.07e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 985
       16.01 -    32.02: 29
       32.02 -    48.03: 12
       48.03 -    64.04: 3
       64.04 -    80.05: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   69.42  -69.42     1      3.00e+01 1.11e-03 6.92e+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   67.80  -67.80     1      3.00e+01 1.11e-03 6.64e+00
  dihedral model="   0" pdb=" CE1 TYR A  50 "
           model="   0" pdb=" CZ  TYR A  50 "
           model="   0" pdb=" OH  TYR A  50 "
           model="   0" pdb=" HH  TYR A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   99.95   80.05     2      3.00e+01 1.11e-03 5.17e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 113
       0.028 -    0.055: 46
       0.055 -    0.083: 6
       0.083 -    0.110: 8
       0.110 -    0.138: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.55e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.015 5.00e-02 4.00e+02   2.34e-02 8.75e-01
        model="   0" pdb=" N   PRO A   6 "   -0.040 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.013 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.009 2.00e-02 2.50e+03   4.22e-03 5.35e-01
        model="   0" pdb=" CG  TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "   -0.012 5.00e-02 4.00e+02   1.79e-02 5.15e-01
        model="   0" pdb=" N   PRO A  54 "    0.031 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "   -0.009 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "   -0.010 5.00e-02 4.00e+02
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 195
        2.23 -     2.82: 4829
        2.82 -     3.41: 5826
        3.41 -     4.01: 7529
        4.01 -     4.60: 11394
  Nonbonded interactions: 29773
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.633 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  63 "
            model="   0" pdb=" OD2 ASP A  88 "
     model   vdw
     1.646 1.850
  nonbonded model="   0" pdb=" HB3 ALA A  48 "
            model="   0" pdb="HH11 ARG A 127 "
     model   vdw
     1.695 2.270
  nonbonded model="   0" pdb="HD13 LEU A  93 "
            model="   0" pdb=" HA2 GLY A  96 "
     model   vdw
     1.748 2.440
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.782 2.270
  ... (remaining 29768 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

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

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.97, 47.568, 50.518, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

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

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: 0.62
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 71
        1.23 -     1.42: 401
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.08e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.41e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.28e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.11e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.80e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       97.50 -   103.80: 17
      103.80 -   110.09: 2136
      110.09 -   116.38: 873
      116.38 -   122.67: 750
      122.67 -   128.97: 303
  Bond angle restraints: 4079
  Sorted by residual:
  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  126.01    5.19 1.30e+00 5.92e-01 1.59e+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  118.62    3.98 1.00e+00 1.00e+00 1.58e+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  126.66    4.54 1.30e+00 5.92e-01 1.22e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.13    3.47 1.00e+00 1.00e+00 1.20e+01
  angle model="   0" pdb=" CA  HIS A 136 "
        model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
      ideal   model   delta    sigma   weight residual
     113.80  110.45    3.35 1.00e+00 1.00e+00 1.12e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 966
       17.57 -    35.15: 49
       35.15 -    52.72: 11
       52.72 -    70.30: 3
       70.30 -    87.87: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A 123 "
           model="   0" pdb=" C   GLU A 123 "
           model="   0" pdb=" N   ALA A 124 "
           model="   0" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.80   31.20     0      5.00e+00 4.00e-02 3.89e+01
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.06   24.94     0      5.00e+00 4.00e-02 2.49e+01
  dihedral model="   0" pdb=" CA  ILE A 122 "
           model="   0" pdb=" C   ILE A 122 "
           model="   0" pdb=" N   GLU A 123 "
           model="   0" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.64   24.36     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 75
       0.050 -    0.099: 64
       0.099 -    0.148: 30
       0.148 -    0.197: 5
       0.197 -    0.246: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 136 "
            model="   0" pdb=" N   HIS A 136 "
            model="   0" pdb=" C   HIS A 136 "
            model="   0" pdb=" CB  HIS A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.35e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.073 2.00e-02 2.50e+03   3.23e-02 3.14e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.066 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 "   -0.025 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 "   -0.020 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   2.38e-02 1.70e+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 "    0.014 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 105 "    0.047 2.00e-02 2.50e+03   1.82e-02 9.89e+00
        model="   0" pdb=" CG  TYR A 105 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 105 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 105 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 105 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 105 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 105 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 105 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 105 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 105 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 157
        2.19 -     2.79: 4357
        2.79 -     3.40: 6057
        3.40 -     4.00: 7300
        4.00 -     4.60: 11174
  Nonbonded interactions: 29045
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.589 1.850
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" OE1 GLU A  84 "
     model   vdw
     1.590 2.450
  nonbonded model="   0" pdb="HD21 LEU A  39 "
            model="   0" pdb="HG21 VAL A 126 "
     model   vdw
     1.610 2.440
  nonbonded model="   0" pdb=" HG  LEU A  39 "
            model="   0" pdb=" HE2 MET A 128 "
     model   vdw
     1.655 2.440
  nonbonded model="   0" pdb=" HZ2 LYS A 109 "
            model="   0" pdb=" OD1 ASP A 110 "
     model   vdw
     1.707 1.850
  ... (remaining 29040 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: 1.22 seconds

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


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

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

  Time building geometry restraints manager: 1.17 seconds

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

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (76.366, 42.529, 44.934, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 103
        1.23 -     1.43: 369
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.08e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.64e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.14e+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 6.73e+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 6.22e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.80 -   105.66: 63
      105.66 -   111.52: 2449
      111.52 -   117.38: 549
      117.38 -   123.24: 823
      123.24 -   129.10: 195
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 138 "
        model="   0" pdb=" CG  HIS A 138 "
        model="   0" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  126.33    4.87 1.30e+00 5.92e-01 1.41e+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  126.51    4.69 1.30e+00 5.92e-01 1.30e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.52    4.68 1.30e+00 5.92e-01 1.30e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.04    3.56 1.00e+00 1.00e+00 1.27e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.70    4.50 1.30e+00 5.92e-01 1.20e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 975
       17.85 -    35.69: 41
       35.69 -    53.54: 11
       53.54 -    71.39: 4
       71.39 -    89.24: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.70   28.30     0      5.00e+00 4.00e-02 3.20e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.46   26.54     0      5.00e+00 4.00e-02 2.82e+01
  dihedral model="   0" pdb=" CA  LEU A  93 "
           model="   0" pdb=" C   LEU A  93 "
           model="   0" pdb=" N   GLY A  94 "
           model="   0" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.62   18.38     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 80
       0.042 -    0.084: 50
       0.084 -    0.126: 32
       0.126 -    0.168: 12
       0.168 -    0.210: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LEU A 119 "
            model="   0" pdb=" N   LEU A 119 "
            model="   0" pdb=" C   LEU A 119 "
            model="   0" pdb=" CB  LEU A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.37e-01
  chirality model="   0" pdb=" CG  LEU A 132 "
            model="   0" pdb=" CB  LEU A 132 "
            model="   0" pdb=" CD1 LEU A 132 "
            model="   0" pdb=" CD2 LEU A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.60e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "   -0.098 2.00e-02 2.50e+03   3.93e-02 4.63e+01
        model="   0" pdb=" CG  PHE A  15 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "   -0.052 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.048 2.00e-02 2.50e+03   2.17e-02 1.41e+01
        model="   0" pdb=" CG  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.045 2.00e-02 2.50e+03   1.86e-02 1.04e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.008 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 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.005 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 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 50
        2.00 -     2.65: 29  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 11
        1.23 -     1.42: 452
        1.42 -     1.61: 669
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ILE A 131 "
       model="   0" pdb=" N   LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.40e-02 5.10e+03 2.92e+00
  bond model="   0" pdb=" C   MET A   1 "
       model="   0" pdb=" N   LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.352 -0.023 1.40e-02 5.10e+03 2.66e+00
  bond model="   0" pdb=" C   ILE A  71 "
       model="   0" pdb=" N   ASN A  72 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.60e+00
  bond model="   0" pdb=" C   SER A  76 "
       model="   0" pdb=" N   ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.46e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.41e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.09 -   106.24: 46
      106.24 -   112.40: 2697
      112.40 -   118.56: 451
      118.56 -   124.71: 842
      124.71 -   130.87: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  104.14    4.86 3.00e+00 1.11e-01 2.63e+00
  angle model="   0" pdb=" CB  PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.68   -4.68 3.00e+00 1.11e-01 2.43e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.67   -4.67 3.00e+00 1.11e-01 2.42e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.56   -4.56 3.00e+00 1.11e-01 2.31e+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  105.48    4.52 3.00e+00 1.11e-01 2.27e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 980
       17.86 -    35.72: 23
       35.72 -    53.58: 10
       53.58 -    71.44: 7
       71.44 -    89.30: 13
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.30   89.30     1      3.00e+01 1.11e-03 1.05e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.80  -88.80     1      3.00e+01 1.11e-03 1.04e+01
  dihedral model="   0" pdb=" CB  GLU A 120 "
           model="   0" pdb=" CG  GLU A 120 "
           model="   0" pdb=" CD  GLU A 120 "
           model="   0" pdb=" OE1 GLU A 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.72   88.72     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.028: 105
       0.028 -    0.055: 52
       0.055 -    0.082: 7
       0.082 -    0.109: 8
      07
        2.65 -     3.30: 6701
        3.30 -     3.95: 7876
        3.95 -     4.60: 12080
  Nonbonded interactions: 29614
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  86 "
            model="   0" pdb=" HB2 TYR A  89 "
     model   vdw
     1.352 2.440
  nonbonded model="   0" pdb=" HB3 LEU A  70 "
            model="   0" pdb="HD11 ILE A  78 "
     model   vdw
     1.393 2.440
  nonbonded model="   0" pdb=" HH  TYR A  12 "
            model="   0" pdb=" HE1 TYR A  89 "
     model   vdw
     1.446 2.100
  nonbonded model="   0" pdb=" HE1 PHE A  15 "
            model="   0" pdb=" HB3 TYR A  81 "
     model   vdw
     1.571 2.270
  nonbonded model="   0" pdb="HD12 ILE A  78 "
            model="   0" pdb="HD22 LEU A  99 "
     model   vdw
     1.610 2.440
  ... (remaining 29609 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
 0.109 -    0.136: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  37 "
            model="   0" pdb=" N   ILE A  37 "
            model="   0" pdb=" C   ILE A  37 "
            model="   0" pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-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    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.66e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.011 2.00e-02 2.50e+03   5.15e-03 7.96e-01
        model="   0" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 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 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 135 "   -0.007 2.00e-02 2.50e+03   5.35e-03 5.72e-01
        model="   0" pdb=" CG  HIS A 135 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 135 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 135 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 135 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 135 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 135 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 135 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.002 2.00e-02 2.50e+03   3.88e-03 4.51e-01
        model="   0" pdb=" CG  TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.07: 64
        2.07 -     2.70: 3633
        2.70 -     3.33: 6440
        3.33 -     3.97: 8112
        3.97 -     4.60: 12540
  Nonbonded interactions: 30789
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  78 "
            model="   0" pdb=" HD2 TYR A  91 "
     model   vdw
     1.433 2.270
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HH  TYR A  89 "
     model   vdw
     1.564 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.572 1.850
  nonbonded model="   0" pdb="HD12 ILE A  78 "
            model="   0" pdb=" HD2 TYR A  91 "
     model   vdw
     1.573 2.270
  nonbonded model="   0" pdb=" H   GLY A  96 "
            model="   0" pdb=" H   SER A  97 "
     model   vdw
     1.639 2.100
  ... (remaining 30784 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.632, 41.726, 65.445, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

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

============================== 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: 1.09
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.23 seconds

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

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

  Time building geometry restraints manager: 1.11 seconds

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

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (64.105, 42.09, 80.558, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 83
        1.23 -     1.43: 389
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 8.46e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.92e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.64e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.32e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.25e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.21 -   105.97: 99
      105.97 -   111.74: 2440
      111.74 -   117.50: 541
      117.50 -   123.27: 808
      123.27 -   129.03: 191
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.79   -4.19 1.00e+00 1.00e+00 1.76e+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  118.60    4.00 1.00e+00 1.00e+00 1.60e+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  116.57   -3.97 1.00e+00 1.00e+00 1.57e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.90    3.70 1.00e+00 1.00e+00 1.37e+01
  angle model="   0" pdb=" 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  126.40    4.80 1.30e+00 5.92e-01 1.36e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.79: 969
       16.79 -    33.57: 48
       33.57 -    50.36: 13
       50.36 -    67.15: 2
       67.15 -    83.93: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A 122 "
           model="   0" pdb=" C   ILE A 122 "
           model="   0" pdb=" N   GLU A 123 "
           model="   0" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.93   33.07     0      5.00e+00 4.00e-02 4.38e+01
  dihedral model="   0" pdb=" CA  ARG A 127 "
           model="   0" pdb=" C   ARG A 127 "
           model="   0" pdb=" N   MET A 128 "
           model="   0" pdb=" CA  MET A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.11   30.89     0      5.00e+00 4.00e-02 3.82e+01
  dihedral model="   0" pdb=" CA  LYS A 125 "
           model="   0" pdb=" C   LYS A 125 "
           model="   0" pdb=" N   VAL A 126 "
           model="   0" pdb=" CA  VAL A 126 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.78   26.22     0      5.00e+00 4.00e-02 2.75e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 69
       0.039 -    0.077: 40
       0.077 -    0.115: 38
       0.115 -    0.153: 25
       0.153 -    0.191: 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 9.08e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.76e-01
  chirality model="   0" pdb=" CG  LEU A  99 "
            model="   0" pdb=" CB  LEU A  99 "
            model="   0" pdb=" CD1 LEU A  99 "
            model="   0" pdb=" CD2 LEU A  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.08e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.062 2.00e-02 2.50e+03   2.76e-02 2.29e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.003 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 "   -0.021 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 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.063 2.00e-02 2.50e+03   2.50e-02 1.88e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.017 2.00e-02 2.50e+03   3.52e-02 1.24e+01
        model="   0" pdb=" CG  ASP A  36 "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.021 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 87
        2.13 -     2.75: 3882
        2.75 -     3.37: 6052
        3.37 -     3.98: 7311
        3.98 -     4.60: 11070
  Nonbonded interactions: 28402
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A  32 "
            model="   0" pdb=" H   THR A  92 "
     model   vdw
     1.515 1.850
  nonbonded model="   0" pdb=" OH  TYR A  68 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.676 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.678 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.702 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.747 1.850
  ... (remaining 28397 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: 9
        1.23 -     1.42: 455
        1.42 -     1.61: 668
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ILE A 122 "
       model="   0" pdb=" N   GLU A 123 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.92e+00
  bond model="   0" pdb=" C   PRO A 117 "
       model="   0" pdb=" N   ASP A 118 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.69e+00
  bond model="   0" pdb=" C   HIS A 134 "
       model="   0" pdb=" N   HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.63e+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 1.59e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.53e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.65 -   106.71: 51
      106.71 -   112.76: 2724
      112.76 -   118.81: 429
      118.81 -   124.87: 833
      124.87 -   130.92: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.95   -4.95 3.00e+00 1.11e-01 2.72e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.48   -4.48 3.00e+00 1.11e-01 2.23e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.48   -4.48 3.00e+00 1.11e-01 2.23e+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  104.68    4.32 3.00e+00 1.11e-01 2.07e+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  104.76    4.24 3.00e+00 1.11e-01 2.00e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 990
       17.29 -    34.58: 19
       34.58 -    51.87: 11
       51.87 -    69.15: 3
       69.15 -    86.44: 10
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A 133 "
           model="   0" pdb=" CG  GLU A 133 "
           model="   0" pdb=" CD  GLU A 133 "
           model="   0" pdb=" OE1 GLU A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.44   86.44     1      3.00e+01 1.11e-03 1.00e+01
  dihedral model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" CB  ASP A 116 "
           model="   0" pdb=" CG  ASP A 116 "
           model="   0" pdb=" OD1 ASP A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.68   51.68     1      2.00e+01 2.50e-03 9.12e+00
  dihedral model="   0" pdb=" CB  GLU A  84 "
           model="   0" pdb=" CG  GLU A  84 "
           model="   0" pdb=" CD  GLU A  84 "
           model="   0" pdb=" OE1 GLU A  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   81.42  -81.42     1      3.00e+01 1.11e-03 9.07e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 122
       0.031 -    0.063: 38
       0.063 -    0.094: 6
       0.094 -    0.125: 7
       0.125 -    0.157: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.14e-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    2.59   -0.15 2.00e-01 2.50e+01 5.86e-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    2.58   -0.15 2.00e-01 2.50e+01 5.27e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 138 "   -0.006 2.00e-02 2.50e+03   5.43e-03 5.89e-01
        model="   0" pdb=" CG  HIS A 138 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 138 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 138 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 138 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 138 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 138 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 138 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.008 2.00e-02 2.50e+03   4.33e-03 5.62e-01
        model="   0" pdb=" CG  TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.006 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 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.009 2.00e-02 2.50e+03   3.85e-03 4.45e-01
        model="   0" pdb=" CG  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 165
        2.21 -     2.81: 4663
        2.81 -     3.41: 5677
        3.41 -     4.00: 7117
        4.00 -     4.60: 10826
  Nonbonded interactions: 28448
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.613 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  29 "
            model="   0" pdb="HD22 ASN A  72 "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb=" HA  GLU A  75 "
            model="   0" pdb="HG22 ILE A  78 "
     model   vdw
     1.728 2.440
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.762 2.270
  nonbonded model="   0" pdb="HG13 VAL A 126 "
            model="   0" pdb=" HG3 ARG A 129 "
     model   vdw
     1.789 2.440
  ... (remaining 28443 not shown)

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

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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (70.825, 43.505, 44.528, 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     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.77 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 102
        1.23 -     1.43: 370
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.88e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.43e+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 5.31e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.27e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.17e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.21 -   106.71: 154
      106.71 -   112.21: 2510
      112.21 -   117.71: 416
      117.71 -   123.21: 802
      123.21 -   128.71: 197
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.38   -3.78 1.00e+00 1.00e+00 1.43e+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 1.24e+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  115.98   -3.38 1.00e+00 1.00e+00 1.14e+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  119.45    3.15 1.00e+00 1.00e+00 9.90e+00
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.71   -4.31 1.40e+00 5.10e-01 9.47e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 976
       17.99 -    35.99: 33
       35.99 -    53.98: 18
       53.98 -    71.97: 5
       71.97 -    89.96: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.39   20.61     0      5.00e+00 4.00e-02 1.70e+01
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.10   18.90     0      5.00e+00 4.00e-02 1.43e+01
  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  161.16   18.84     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 86
       0.054 -    0.108: 57
       0.108 -    0.162: 29
       0.162 -    0.216: 3
       0.216 -    0.270: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.46e-01
  chirality model="   0" pdb=" CA  ASP A  74 "
            model="   0" pdb=" N   ASP A  74 "
            model="   0" pdb=" C   ASP A  74 "
            model="   0" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.19 2.00e-01 2.50e+01 8.57e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.072 2.00e-02 2.50e+03   3.25e-02 3.17e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 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 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.069 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 "   -0.025 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 "   -0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.022 2.00e-02 2.50e+03   4.51e-02 2.04e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.078 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.049 2.00e-02 2.50e+03   1.87e-02 1.05e+01
        model="   0" pdb=" CG  TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 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 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 151
        2.19 -     2.79: 4293
        2.79 -     3.40: 6121
        3.40 -     4.00: 7340
        4.00 -     4.60: 10947
  Nonbonded interactions: 28852
  Sorted by model distance:
  nonbonded model="   0" pdb=" HG  SER A  17 "
            model="   0" pdb=" OE2 GLU A  84 "
     model   vdw
     1.590 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.668 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.680 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.744 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.761 1.850
  ... (remaining 28847 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

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

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

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


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

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

  Time building geometry restraints manager: 1.14 seconds

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

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

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

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

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

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 1.10 seconds

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 4
        1.23 -     1.42: 461
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A  43 "
       model="   0" pdb=" N   ASP A  44 "
    ideal  model  delta    sigma   weight residual
    1.329  1.350 -0.021 1.40e-02 5.10e+03 2.19e+00
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.204  0.027 2.00e-02 2.50e+03 1.84e+00
  bond model="   0" pdb=" C   ALA A 115 "
       model="   0" pdb=" N   ASP A 116 "
    ideal  model  delta    sigma   weight residual
    1.329  1.348 -0.019 1.40e-02 5.10e+03 1.76e+00
  bond model="   0" pdb=" C   ASP A  47 "
       model="   0" pdb=" N   ALA A  48 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.48e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.48e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.82 -   106.92: 81
      106.92 -   113.01: 2687
      113.01 -   119.10: 442
      119.10 -   125.20: 827
      125.20 -   131.29: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.82    5.18 3.00e+00 1.11e-01 2.98e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  104.92    5.08 3.00e+00 1.11e-01 2.87e+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  114.02   -5.02 3.00e+00 1.11e-01 2.80e+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  113.92   -4.92 3.00e+00 1.11e-01 2.69e+00
  angle model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" CA  GLY A  80 "
        model="   0" pdb=" C   GLY A  80 "
      ideal   model   delta    sigma   weight residual
     113.30  118.04   -4.74 2.90e+00 1.19e-01 2.67e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 990
       17.73 -    35.47: 26
       35.47 -    53.20: 10
       53.20 -    70.94: 2
       70.94 -    88.67: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.67   88.67     1      3.00e+01 1.11e-03 1.04e+01
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.70   87.70     1      3.00e+01 1.11e-03 1.02e+01
  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  -79.80   79.80     1      3.00e+01 1.11e-03 8.78e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 111
       0.033 -    0.066: 47
       0.066 -    0.098: 13
       0.098 -    0.131: 1
       0.131 -    0.164: 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    2.60   -0.16 2.00e-01 2.50e+01 6.73e-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    2.58   -0.15 2.00e-01 2.50e+01 5.45e-01
  chirality model="   0" pdb=" CB  ILE A  86 "
            model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" CG1 ILE A  86 "
            model="   0" pdb=" CG2 ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.25e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.017 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  91 "   -0.010 2.00e-02 2.50e+03   5.93e-03 1.06e+00
        model="   0" pdb=" CG  TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.010 2.00e-02 2.50e+03   5.62e-03 9.46e-01
        model="   0" pdb=" CG  TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.012 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 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 51
        2.08 -     2.71: 3709
        2.71 -     3.34: 6108
        3.34 -     3.97: 7659
        3.97 -     4.60: 12001
  Nonbonded interactions: 29528
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LEU A  93 "
            model="   0" pdb="HD23 LEU A  99 "
     model   vdw
     1.451 2.620
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb="HG13 ILE A  86 "
     model   vdw
     1.506 2.270
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb="HG12 ILE A  86 "
     model   vdw
     1.577 2.270
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.718 1.850
  nonbonded model="   0" pdb=" HG  SER A  13 "
            model="   0" pdb=" OE1 GLN A  66 "
     model   vdw
     1.721 1.850
  ... (remaining 29523 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: 112
        1.23 -     1.43: 360
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.18e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.65e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.41e+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 5.32e+00
  bond model="   0" pdb=" C   GLY A  80 "
       model="   0" pdb=" N   TYR A  81 "
    ideal  model  delta    sigma   weight residual
    1.329  1.361 -0.032 1.40e-02 5.10e+03 5.24e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.61 -   106.25: 115
      106.25 -   111.89: 2491
      111.89 -   117.53: 468
      117.53 -   123.16: 796
      123.16 -   128.80: 209
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.60    4.00 1.00e+00 1.00e+00 1.60e+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  128.80   -7.10 1.80e+00 3.09e-01 1.56e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.31   -3.71 1.00e+00 1.00e+00 1.38e+01
  angle model="   0" pdb=" C   THR A  82 "
        model="   0" pdb=" N   THR A  83 "
        model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  128.33   -6.63 1.80e+00 3.09e-01 1.36e+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  126.41    4.79 1.30e+00 5.92e-01 1.36e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 956
       17.47 -    34.94: 59
       34.94 -    52.40: 12
       52.40 -    69.87: 4
       69.87 -    87.34: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  94 "
           model="   0" pdb=" C   GLY A  94 "
           model="   0" pdb=" N   ASP A  95 "
           model="   0" pdb=" CA  ASP A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.12  -26.88     0      5.00e+00 4.00e-02 2.89e+01
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.42   24.58     0      5.00e+00 4.00e-02 2.42e+01
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.25   22.75     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 69
       0.037 -    0.075: 43
       0.075 -    0.112: 32
       0.112 -    0.149: 28
       0.149 -    0.186: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A  95 "
            model="   0" pdb=" N   ASP A  95 "
            model="   0" pdb=" C   ASP A  95 "
            model="   0" pdb=" CB  ASP A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.65e-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    2.61   -0.18 2.00e-01 2.50e+01 8.03e-01
  chirality model="   0" pdb=" CA  HIS A 134 "
            model="   0" pdb=" N   HIS A 134 "
            model="   0" pdb=" C   HIS A 134 "
            model="   0" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.71e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.060 2.00e-02 2.50e+03   2.37e-02 1.69e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.040 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 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "   -0.040 2.00e-02 2.50e+03   1.78e-02 9.55e+00
        model="   0" pdb=" CG  TYR A  68 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 "   -0.030 2.00e-02 2.50e+03   1.78e-02 6.34e+00
        model="   0" pdb=" CG  HIS A 139 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 "    0.005 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 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.27: 267
        2.27 -     2.85: 4918
        2.85 -     3.43: 5380
        3.43 -     4.02: 6856
        4.02 -     4.60: 10287
  Nonbonded interactions: 27708
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.685 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.843 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.849 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.850 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.852 1.850
  ... (remaining 27703 not shown)

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  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: 0.96, per 1000 atoms: 0.43
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.809, 57.765, 64.191, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 0.94, per 1000 atoms: 0.42
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (71.604, 41.828, 66.343, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 6
        1.23 -     1.42: 459
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.389 -0.015 1.10e-02 8.26e+03 1.86e+00
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.82e+00
  bond model="   0" pdb=" C   LYS A 125 "
       model="   0" pdb=" N   VAL A 126 "
    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   HIS A 135 "
       model="   0" pdb=" N   HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.28e+00
  bond model="   0" pdb=" C   TYR A  81 "
       model="   0" pdb=" N   THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.015 1.40e-02 5.10e+03 1.20e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.62 -   106.70: 59
      106.70 -   112.78: 2708
      112.78 -   118.86: 439
      118.86 -   124.94: 831
      124.94 -   131.03: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.96   -4.96 3.00e+00 1.11e-01 2.73e+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  104.33    4.67 3.00e+00 1.11e-01 2.42e+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  105.39    4.61 3.00e+00 1.11e-01 2.36e+00
  angle model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" CB  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     111.60  108.57    3.03 2.00e+00 2.50e-01 2.30e+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  105.50    4.50 3.00e+00 1.11e-01 2.25e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 993
       16.49 -    32.97: 18
       32.97 -    49.46: 11
       49.46 -    65.94: 6
       65.94 -    82.43: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   82.43  -82.43     1      3.00e+01 1.11e-03 9.26e+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  -76.51   76.51     1      3.00e+01 1.11e-03 8.18e+00
  dihedral model="   0" pdb=" CA  ASP A  47 "
           model="   0" pdb=" CB  ASP A  47 "
           model="   0" pdb=" CG  ASP A  47 "
           model="   0" pdb=" OD1 ASP A  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -74.52   44.52     1      2.00e+01 2.50e-03 6.89e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 100
       0.030 -    0.061: 57
       0.061 -    0.091: 7
       0.091 -    0.121: 6
       0.121 -    0.152: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.74e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.34e-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    2.58   -0.15 2.00e-01 2.50e+01 5.28e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.015 5.00e-02 4.00e+02   2.32e-02 8.61e-01
        model="   0" pdb=" N   PRO A   6 "   -0.040 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.013 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.011 2.00e-02 2.50e+03   5.07e-03 7.70e-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 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.002 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 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "    0.011 2.00e-02 2.50e+03   4.23e-03 5.36e-01
        model="   0" pdb=" CG  TYR A  68 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 210
        2.25 -     2.83: 5026
        2.83 -     3.42: 5523
        3.42 -     4.01: 7375
        4.01 -     4.60: 10851
  Nonbonded interactions: 28985
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A  32 "
            model="   0" pdb="HD21 ASN A  72 "
     model   vdw
     1.658 1.850
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" O   ASP A  44 "
     model   vdw
     1.799 2.620
  nonbonded model="   0" pdb=" HZ1 LYS A  63 "
            model="   0" pdb=" HD1 TYR A  89 "
     model   vdw
     1.802 2.100
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.843 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.847 2.270
  ... (remaining 28980 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.91, per 1000 atoms: 0.41
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.098, 61.406, 45.968, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.19 seconds

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

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (77.254, 42.268, 67.959, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 94
        1.23 -     1.43: 378
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.353 -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  1.296  0.034 1.30e-02 5.92e+03 6.91e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.45e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.05e+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 5.96e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.29 -   106.03: 83
      106.03 -   111.77: 2496
      111.77 -   117.51: 496
      117.51 -   123.25: 809
      123.25 -   128.99: 195
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.40    4.20 1.00e+00 1.00e+00 1.76e+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  118.92    3.68 1.00e+00 1.00e+00 1.35e+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  126.61    4.59 1.30e+00 5.92e-01 1.25e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.12   -3.52 1.00e+00 1.00e+00 1.24e+01
  angle model="   0" pdb=" 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 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.35: 955
       16.35 -    32.69: 60
       32.69 -    49.04: 11
       49.04 -    65.39: 5
       65.39 -    81.73: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.46  -16.54     0      5.00e+00 4.00e-02 1.09e+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  164.33   15.67     0      5.00e+00 4.00e-02 9.82e+00
  dihedral model="   0" pdb=" N   ASP A  95 "
           model="   0" pdb=" CA  ASP A  95 "
           model="   0" pdb=" CB  ASP A  95 "
           model="   0" pdb=" CG  ASP A  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.54  -54.46     3      1.50e+01 4.44e-03 9.28e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 73
       0.039 -    0.078: 45
       0.078 -    0.118: 34
       0.118 -    0.157: 20
     
  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

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

  0.157 -    0.196: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.58e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.48e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.95e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.069 2.00e-02 2.50e+03   2.97e-02 2.65e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.025 2.00e-02 2.50e+03   5.03e-02 2.53e+01
        model="   0" pdb=" CG  ASP A  36 "    0.087 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.030 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.052 2.00e-02 2.50e+03   2.00e-02 1.20e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 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 "   -0.014 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 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.02: 40
        2.02 -     2.67: 3075
        2.67 -     3.31: 6529
        3.31 -     3.96: 7848
        3.96 -     4.60: 11664
  Nonbonded interactions: 29156
  Sorted by model distance:
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" HE2 TYR A  81 "
     model   vdw
     1.380 2.100
  nonbonded model="   0" pdb=" O   TYR A  81 "
            model="   0" pdb=" O   LEU A  93 "
     model   vdw
     1.396 2.800
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.483 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.707 1.850
  nonbonded model="   0" pdb="HD21 LEU A  93 "
            model="   0" pdb="HD13 LEU A  99 "
     model   vdw
     1.721 2.440
  ... (remaining 29151 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

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

  Time building chain proxies: 1.04, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.329, 43.527, 57.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 83
        1.23 -     1.43: 389
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.41e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.16e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 6.96e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.79e+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 6.73e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.17 -   106.00: 84
      106.00 -   111.84: 2506
      111.84 -   117.67: 487
      117.67 -   123.51: 861
      123.51 -   129.34: 141
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.69    3.91 1.00e+00 1.00e+00 1.53e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.36    4.84 1.30e+00 5.92e-01 1.39e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.05    3.55 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.59    4.61 1.30e+00 5.92e-01 1.26e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.12   -3.52 1.00e+00 1.00e+00 1.24e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 961
       16.00 -    32.01: 49
       32.01 -    48.01: 16
       48.01 -    64.02: 4
       64.02 -    80.02: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.19   23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.51   18.49     0      5.00e+00 4.00e-02 1.37e+01
  dihedral model="   0" pdb=" CA  SER A  98 "
           model="   0" pdb=" C   SER A  98 "
           model="   0" pdb=" N   LEU A  99 "
           model="   0" pdb=" CA  LEU A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.38   16.62     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.041: 77
       0.041 -    0.081: 39
       0.081 -    0.121: 39
       0.121 -    0.161: 18
       0.161 -    0.201: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.14e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.93e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.077 2.00e-02 2.50e+03   3.39e-02 3.46e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.070 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.025 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 "    0.020 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 "    0.013 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 "    0.012 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 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.030 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 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "    0.044 2.00e-02 2.50e+03   1.82e-02 9.90e+00
        model="   0" pdb=" CG  PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "    0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 123
        2.17 -     2.77: 4121
        2.77 -     3.38: 6147
        3.38 -     3.99: 7369
        3.99 -     4.60: 11150
  Nonbonded interactions: 28910
  Sorted by model distance:
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" HD1 TYR A  91 "
     model   vdw
     1.557 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.634 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.784 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.804 1.850
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" CD1 TYR A  91 "
     model   vdw
     1.817 2.970
  ... (remaining 28905 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (84.005, 45.639, 45.147, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.15 seconds

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 64
        1.23 -     1.42: 408
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.385 -0.031 1.10e-02 8.26e+03 7.88e+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 7.78e+00
  bond model="   0" pdb=" C   ILE A 131 "
       model="   0" pdb=" N   LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.364 -0.035 1.40e-02 5.10e+03 6.34e+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 6.18e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.27 -   106.04: 86
      106.04 -   111.80: 2508
      111.80 -   117.57: 484
      117.57 -   123.34: 815
      123.34 -   129.11: 186
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.32    4.28 1.00e+00 1.00e+00 1.83e+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  118.84    3.76 1.00e+00 1.00e+00 1.41e+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  126.42    4.78 1.30e+00 5.92e-01 1.35e+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  126.49    4.71 1.30e+00 5.92e-01 1.31e+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  116.00   -3.40 1.00e+00 1.00e+00 1.16e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 964
       17.02 -    34.05: 47
       34.05 -    51.07: 16
       51.07 -    68.10: 4
       68.10 -    85.12: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.46  -21.54     0      5.00e+00 4.00e-02 1.86e+01
  dihedral model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
           model="   0" pdb=" CB  HIS A 139 "
           model="   0" pdb=" CG  HIS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.29   58.29     3      1.50e+01 4.44e-03 9.46e+00
  dihedral model="   0" pdb=" N   ARG A 129 "
           model="   0" pdb=" CA  ARG A 129 "
           model="   0" pdb=" CB  ARG A 129 "
           model="   0" pdb=" CG  ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.61  -57.39     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 77
       0.043 -    0.086: 43
       0.086 -    0.128: 37
       0.128 -    0.171: 17
       0.171 -    0.214: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.70e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.076 2.00e-02 2.50e+03   3.10e-02 2.87e+01
        model="   0" pdb=" CG  TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.067 2.00e-02 2.50e+03   2.95e-02 2.61e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.011 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 "   -0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.053 2.00e-02 2.50e+03   2.08e-02 1.30e+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 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.20: 167
        2.20 -     2.80: 4353
        2.80 -     3.40: 6096
        3.40 -     4.00: 7347
        4.00 -     4.60: 11179
  Nonbonded interactions: 29142
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.594 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.634 1.850
  nonbonded model="   0" pdb="HG22 ILE A  77 "
            model="   0" pdb=" HE2 TYR A  81 "
     model   vdw
     1.719 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.739 1.850
  ... (remaining 29137 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.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 7
        1.23 -     1.42: 458
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.390 -0.016 1.10e-02 8.26e+03 2.06e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.51e+00
  bond model="   0" pdb=" C   PRO A 114 "
       model="   0" pdb=" N   ALA A 115 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.49e+00
  bond model="   0" pdb=" C   HIS A 136 "
       model="   0" pdb=" N   HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.28e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.332 -0.011 1.00e-02 1.00e+04 1.21e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.55 -   106.63: 52
      106.63 -   112.70: 2722
      112.70 -   118.78: 431
      118.78 -   124.85: 832
      124.85 -   130.93: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.84   -4.84 3.00e+00 1.11e-01 2.60e+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  113.74   -4.74 3.00e+00 1.11e-01 2.49e+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  113.49   -4.49 3.00e+00 1.11e-01 2.24e+00
  angle model="   0" pdb=" NE  ARG A 129 "
        model="   0" pdb=" CZ  ARG A 129 "
        model="   0" pdb=" NH1 ARG A 129 "
      ideal   model   delta    sigma   weight residual
     121.50  120.01    1.49 1.00e+00 1.00e+00 2.23e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.40   -4.40 3.00e+00 1.11e-01 2.15e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 986
       16.65 -    33.30: 23
       33.30 -    49.95: 10
       49.95 -    66.60: 10
       66.60 -    83.25: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  75 "
           model="   0" pdb=" CG  GLU A  75 "
           model="   0" pdb=" CD  GLU A  75 "
           model="   0" pdb=" OE1 GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.25  -83.25     1      3.00e+01 1.11e-03 9.41e+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   78.62  -78.62     1      3.00e+01 1.11e-03 8.56e+00
  dihedral model="   0" pdb=" CA  ASP A  47 "
           model="   0" pdb=" CB  ASP A  47 "
           model="   0" pdb=" CG  ASP A  47 "
           model="   0" pdb=" OD1 ASP A  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -71.05   41.05     1      2.00e+01 2.50e-03 5.90e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 120
       0.030 -    0.059: 39
       0.059 -    0.089: 3
       0.089 -    0.118: 10
       0.118 -    0.148: 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    2.58   -0.15 2.00e-01 2.50e+01 5.47e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.015 2.00e-02 2.50e+03   5.90e-03 1.04e+00
        model="   0" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.002 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=" C   THR A   5 "    0.013 5.00e-02 4.00e+02   2.05e-02 6.73e-01
        model="   0" pdb=" N   PRO A   6 "   -0.035 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 "    0.011 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "    0.008 2.00e-02 2.50e+03   3.80e-03 4.34e-01
        model="   0" pdb=" CG  TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 34
        2.03 -     2.67: 3215
        2.67 -     3.32: 6404
        3.32 -     3.96: 7860
        3.96 -     4.60: 11953
  Nonbonded interactions: 29466
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 TYR A  81 "
            model="   0" pdb="HD11 ILE A  86 "
     model   vdw
     1.389 2.440
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" OH  TYR A  89 "
     model   vdw
     1.541 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.603 1.850
  nonbonded model="   0" pdb=" HE2 TYR A  91 "
            model="   0" pdb="HD11 LEU A  93 "
     model   vdw
     1.681 2.270
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" O   ASP A  44 "
     model   vdw
     1.753 2.620
  ... (remaining 29461 not shown)

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

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

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (64.187, 44.26, 67.586, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.574, 63.057, 59.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.06 seconds

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


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

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

  Time building geometry restraints manager: 1.21 seconds

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

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 62
        1.23 -     1.42: 410
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.80e+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 6.27e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.85e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.76e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.70e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.01 -   105.90: 77
      105.90 -   111.79: 2503
      111.79 -   117.68: 498
      117.68 -   123.57: 864
      123.57 -   129.46: 137
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  129.46   -7.76 1.80e+00 3.09e-01 1.86e+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  118.57    4.03 1.00e+00 1.00e+00 1.62e+01
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  128.61   -6.91 1.80e+00 3.09e-01 1.47e+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 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.05    3.55 1.00e+00 1.00e+00 1.26e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 973
       17.92 -    35.84: 41
       35.84 -    53.76: 13
       53.76 -    71.68: 4
       71.68 -    89.60: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.03   29.97     0      5.00e+00 4.00e-02 3.59e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.86   21.14     0      5.00e+00 4.00e-02 1.79e+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 -159.84  -20.16     0      5.00e+00 4.00e-02 1.62e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 77
       0.043 -    0.085: 50
       0.085 -    0.128: 31
       0.128 -    0.171: 14
       Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 97
        1.23 -     1.43: 375
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.10e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.03e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.76e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.58e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.42e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.53 -   106.27: 107
      106.27 -   112.01: 2529
      112.01 -   117.75: 459
      117.75 -   123.49: 822
      123.49 -   129.23: 162
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.42    4.18 1.00e+00 1.00e+00 1.74e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.79    3.81 1.00e+00 1.00e+00 1.45e+01
  angle model="   0" pdb=" C   THR A  82 "
        model="   0" pdb=" N   THR A  83 "
        model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  128.08   -6.38 1.80e+00 3.09e-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  116.14   -3.54 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CA  ASP A  44 "
        model="   0" pdb=" CB  ASP A  44 "
        model="   0" pdb=" CG  ASP A  44 "
      ideal   model   delta    sigma   weight residual
     112.60  116.09   -3.49 1.00e+00 1.00e+00 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 969
       17.13 -    34.26: 43
       34.26 -    51.38: 13
       51.38 -    68.51: 6
       68.51 -    85.64: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.24  -16.76     0      5.00e+00 4.00e-02 1.12e+01
  dihedral model="   0" pdb=" CA  HIS A  43 "
           model="   0" pdb=" C   HIS A  43 "
           model="   0" pdb=" N   ASP A  44 "
           model="   0" pdb=" CA  ASP A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.21   15.79     0      5.00e+00 4.00e-02 9.97e+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
    -180.00 -124.49  -55.51     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 72
       0.035 -    0.070: 30
       0.070 -    0.105: 36
       0.105 -    0.140: 29
      0.171 -    0.213: 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    2.65   -0.21 2.00e-01 2.50e+01 1.14e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.20 2.00e-01 2.50e+01 9.51e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.83e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.086 2.00e-02 2.50e+03   3.62e-02 3.94e+01
        model="   0" pdb=" CG  TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.067 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.080 2.00e-02 2.50e+03   3.48e-02 3.63e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.070 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.062 2.00e-02 2.50e+03   2.48e-02 1.85e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.022 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 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.22: 208
        2.22 -     2.82: 45   0.140 -    0.175: 9
  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    2.34    0.17 2.00e-01 2.50e+01 7.63e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.14e-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 5.75e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.023 2.00e-02 2.50e+03   4.73e-02 2.24e+01
        model="   0" pdb=" CG  ASP A  36 "    0.082 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "    0.072 2.00e-02 2.50e+03   2.73e-02 2.24e+01
        model="   0" pdb=" CG  PHE A  15 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "    0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.054 2.00e-02 2.50e+03   2.30e-02 1.59e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.045 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 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.26 -     1.93: 28
        1.93 -     2.60: 2302
        2.60 -     3.27: 6823
        3.27 -     3.93: 8110
        3.93 -     4.60: 12170
  Nonbonded interactions: 29433
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB2 TYR A  81 "
            model="   0" pdb="HD13 LEU A  93 "
     model   vdw
     1.264 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.429 1.850
  nonbonded model="   0" pdb=" HD1 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.486 2.270
  nonbonded model="   72
        2.82 -     3.41: 6009
        3.41 -     4.01: 7366
        4.01 -     4.60: 11204
  Nonbonded interactions: 29359
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.629 1.850
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.660 1.850
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" HD1 TYR A  91 "
     model   vdw
     1.661 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.708 1.850
  nonbonded model="   0" pdb=" HA  ILE A  86 "
            model="   0" pdb=" HE2 TYR A  89 "
     model   vdw
     1.731 2.270
  ... (remaining 29354 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
0" pdb=" O   TYR A  81 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     1.565 2.620
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.601 1.850
  ... (remaining 29428 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 99
        1.23 -     1.43: 373
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 8.07e+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 6.98e+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 6.91e+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 6.69e+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 6.65e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.47 -   106.14: 104
      106.14 -   111.81: 2485
      111.81 -   117.48: 496
      117.48 -   123.16: 781
      123.16 -   128.83: 213
  Bond angle restraints: 4079
  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  118.99    3.61 1.00e+00 1.00e+00 1.30e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.73    4.47 1.30e+00 5.92e-01 1.18e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.35    3.25 1.00e+00 1.00e+00 1.06e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.83   -4.43 1.40e+00 5.10e-01 1.00e+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  127.21    3.99 1.30e+00 5.92e-01 9.43e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 972
       17.83 -    35.66: 42
       35.66 -    53.49: 15
       53.49 -    71.32: 3
       71.32 -    89.15: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.27   27.73     0      5.00e+00 4.00e-02 3.08e+01
  dihedral model="   0" pdb=" CA  ARG A 129 "
           model="   0" pdb=" C   ARG A 129 "
           model="   0" pdb=" N   SER A 130 "
           model="   0" pdb=" CA  SER A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.75   27.25     0      5.00e+00 4.00e-02 2.97e+01
  dihedral model="   0" pdb=" CA  GLU A 133 "
           model="   0" pdb=" C   GLU A 133 "
           model="   0" pdb=" N   HIS A 134 "
           model="   0" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.93   25.07     0      5.00e+00 4.00e-02 2.51e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.040: 77
       0.040 -    0.080: 46
       0.080 -    0.120: 34
       0.120 -    0.160: 16
       0.160 -    0.199: 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 9.95e-01
  chirality model="   0" pdb=" CG  LEU A  39 "
            model="   0" pdb=" CB  LEU A  39 "
            model="   0" pdb=" CD1 LEU A  39 "
            model="   0" pdb=" CD2 LEU A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.74e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.48e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.058 2.00e-02 2.50e+03   2.43e-02 1.77e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.045 2.00e-02 2.50e+03   2.25e-02 1.51e+01
        model="   0" pdb=" CG  TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.025 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.055 2.00e-02 2.50e+03   2.21e-02 1.46e+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 "   -0.013 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 "    0.039 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 "   -0.017 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
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     1.96: 24
        1.96 -     2.62: 2533
        2.62 -     3.28: 6738
        3.28 -     3.94: 7959
        3.94 -     4.60: 12019
  Nonbonded interactions: 29273
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   VAL A  14 "
            model="   0" pdb="HD12 ILE A  86 "
     model   vdw
     1.296 2.620
  nonbonded model="   0" pdb=" O   ILE A  77 "
            model="   0" pdb=" HA3 GLY A  96 "
     model   vdw
     1.611 2.620
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" OE1 GLU A  84 "
     model   vdw
     1.664 2.450
  nonbonded model="   0" pdb=" O   ASP A  95 "
            model="   0" pdb=" H   SER A  98 "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.735 1.850
  ... (remaining 29268 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.378, 56.036, 49.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 71
        1.23 -     1.43: 401
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.09e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.81e+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 5.63e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.51e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.28e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.48 -   106.17: 101
      106.17 -   111.85: 2503
      111.85 -   117.53: 465
      117.53 -   123.21: 809
      123.21 -   128.89: 201
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.60    4.00 1.00e+00 1.00e+00 1.60e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.17    3.43 1.00e+00 1.00e+00 1.18e+01
  angle model="   0" pdb=" 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  115.96   -3.36 1.00e+00 1.00e+00 1.13e+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  115.88   -3.28 1.00e+00 1.00e+00 1.08e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.97    4.23 1.30e+00 5.92e-01 1.06e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 974
       17.84 -    35.68: 36
       35.68 -    53.52: 19
       53.52 -    71.36: 3
       71.36 -    89.20: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.91   23.09     0      5.00e+00 4.00e-02 2.13e+01
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.72   21.28     0      5.00e+00 4.00e-02 1.81e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.50   15.50     0      5.00e+00 4.00e-02 9.61e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 80
       0.048 -    0.096: 54
       0.096 -    0.143: 32
       0.143 -    0.191: 7
       0.191 -    0.239: 3
  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    2.29    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.070 2.00e-02 2.50e+03   3.06e-02 2.80e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.014 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 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.062 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 "   -0.022 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 "   -0.020 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.061 2.00e-02 2.50e+03   2.38e-02 1.70e+01
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.007 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 "    0.019 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 "    0.008 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  ASP A  36 "   -0.020 2.00e-02 2.50e+03   4.09e-02 1.67e+01
        model="   0" pdb=" CG  ASP A  36 "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.11: 80
        2.11 -     2.73: 3717
        2.73 -     3.35: 6259
        3.35 -     3.98: 7602
        3.98 -     4.60: 11469
  Nonbonded interactions: 29127
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.481 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.682 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.699 1.850
  nonbonded model="   0" pdb="HD11 LEU A  64 "
            model="   0" pdb=" HE3 LYS A 101 "
     model   vdw
     1.705 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.755 1.850
  ... (remaining 29122 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.88, per 1000 atoms: 0.40
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.004, 70.623, 46.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

  Time building geometry restraints manager: 1.10 seconds

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 76
        1.23 -     1.43: 396
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 8.23e+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 7.09e+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 7.06e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.03e+00
  bond model="   0" pdb=" CE1 HIS A 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 6.73e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.28 -   105.99: 71
      105.99 -   111.71: 2491
      111.71 -   117.42: 498
      117.42 -   123.14: 812
      123.14 -   128.85: 207
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.32    4.28 1.00e+00 1.00e+00 1.83e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.23   -3.63 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.62    4.58 1.30e+00 5.92e-01 1.24e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.00   -3.40 1.00e+00 1.00e+00 1.15e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.85   -4.45 1.40e+00 5.10e-01 1.01e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 978
       16.74 -    33.47: 33
       33.47 -    50.21: 14
       50.21 -    66.94: 7
       66.94 -    83.68: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.55   17.45     0      5.00e+00 4.00e-02 1.22e+01
  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 -119.06   59.06     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   0" pdb=" N   HIS A 135 "
           model="   0" pdb=" CA  HIS A 135 "
           model="   0" pdb=" CB  HIS A 135 "
           model="   0" pdb=" CG  HIS A 135 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.44   55.44     3      1.50e+01 4.44e-03 9.35e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 75
       0.039 -    0.078: 42
       0.078 -    0.117: 35
       0.117 -    0.155: 20
       0.155 -    0.194: 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 9.42e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.05e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.78e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.054 2.00e-02 2.50e+03   2.27e-02 1.54e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.011 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 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.011 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 "    0.050 2.00e-02 2.50e+03   1.96e-02 1.15e+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 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 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 "    0.033 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 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.014 2.00e-02 2.50e+03   2.95e-02 8.72e+00
        model="   0" pdb=" CG  ASP A  36 "   -0.051 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.018 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 275
        2.27 -     2.85: 5046
        2.85 -     3.43: 5560
        3.43 -     4.02: 7376
        4.02 -     4.60: 10960
  Nonbonded interactions: 29217
  Sorted by model distance:
  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=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.753 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.756 1.850
  ... (remaining 29212 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: 93
        1.23 -     1.43: 379
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.87e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.60e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.19e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.15e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.10e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.06 -   105.82: 79
      105.82 -   111.58: 2429
      111.58 -   117.34: 545
      117.34 -   123.10: 813
      123.10 -   128.86: 213
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.70    3.90 1.00e+00 1.00e+00 1.52e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.34   -3.74 1.00e+00 1.00e+00 1.40e+01
  angle model="   0" pdb=" 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  126.46    4.74 1.30e+00 5.92e-01 1.33e+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  126.47    4.73 1.30e+00 5.92e-01 1.32e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.16    3.44 1.00e+00 1.00e+00 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 966
       17.14 -    34.27: 43
       34.27 -    51.41: 18
       51.41 -    68.55: 4
       68.55 -    85.68: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.52  -19.48     0      5.00e+00 4.00e-02 1.52e+01
  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  160.98   19.02     0      5.00e+00 4.00e-02 1.45e+01
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.80   17.20     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 68
       0.042 -    0.085: 51
       0.085 -    0.127: 37
       0.127 -    0.169: 16
       0.169 -    0.211: 4
  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    2.32    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    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  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.069 2.00e-02 2.50e+03   3.09e-02 2.86e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 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 "   -0.015 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 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.064 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.021 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        model="   0" pdb=" CG  ASP A  36 "    0.075 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.059 2.00e-02 2.50e+03   2.29e-02 1.57e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 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 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        0.97 -     1.70: 7
        1.70 -     2.42: 1102
        2.42 -     3.15: 6845
        3.15 -     3.87: 8292
        3.87 -     4.60: 12958
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 29204
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   THR A  82 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     0.969 2.620
  nonbonded model="   0" pdb=" O   THR A  92 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.005 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.480 1.850
  nonbonded model="   0" pdb=" OG  SER A  76 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.500 1.850
  nonbonded model="   0" pdb="HG23 THR A  83 "
            model="   0" pdb=" HA  THR A  92 "
     model   vdw
     1.603 2.440
  ... (remaining 29199 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)----------                  


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.665)
  Mean delta:    0.012 (Z=  0.619)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.762 (Z=  4.176)
  Mean delta:    1.577 (Z=  0.867)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.024
  Max. delta:   85.640
  Mean delta:   12.306

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.175
  Mean delta:    0.075

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  36  ASP  CB
   A  36  ASP  CG
   A  36  ASP  OD1
   A  36  ASP  OD2           0.047       0.082       22.42   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.053
  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   2242  Z= 0.441
    Angle     :  1.526   6.762   4079  Z= 0.662
    Chirality :  0.075   0.175    176
    Planarity :  0.009   0.047    327
    Dihedral  : 11.663  85.640    769
    Min Nonbonded Distance : 1.264
  
  Molprobity Statistics.
    All-atom Clashscore : 13.98
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    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: -0.85 (0.70), residues: 137
    helix: -0.12 (0.50), residues: 93
    sheet:  None (None), residues: 0
    loop : -1.31 (1.04), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS A 137 
   PHE   0.064   0.009   PHE A  15 
   TYR   0.056   0.012   TYR A 111 
   ARG   0.043   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS A 137 
   PHE   0.042   0.010   PHE A  15 
   TYR   0.047   0.015   TYR A 111 
   ARG   0.005   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.59
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 1
        1.23 -     1.42: 462
        1.42 -     1.61: 669
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   THR A  92 "
       model="   0" pdb=" N   LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.355 -0.026 1.40e-02 5.10e+03 3.55e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.344 -0.015 1.40e-02 5.10e+03 1.18e+00
  bond model="   0" pdb=" NE  ARG A 129 "
       model="   0" pdb=" CZ  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.326  1.337 -0.011 1.10e-02 8.26e+03 9.99e-01
  bond model="   0" pdb=" C   GLY A  94 "
       model="   0" pdb=" N   ASP A  95 "
    ideal  model  delta    sigma   weight residual
    1.329  1.343 -0.014 1.40e-02 5.10e+03 9.84e-01
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.315  0.014 1.40e-02 5.10e+03 9.74e-01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.50 -   106.56: 52
      106.56 -   112.62: 2707
      112.62 -   118.68: 441
      118.68 -   124.74: 835
      124.74 -   130.80: 44
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.08   -5.08 3.00e+00 1.11e-01 2.86e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.78   -4.78 3.00e+00 1.11e-01 2.54e+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  104.32    4.68 3.00e+00 1.11e-01 2.43e+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  104.46    4.54 3.00e+00 1.11e-01 2.29e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.42   -4.42 3.00e+00 1.11e-01 2.17e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 985
       16.73 -    33.47: 22
       33.47 -    50.20: 11
       50.20 -    66.93: 8
       66.93 -    83.66: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A  36 "
           model="   0" pdb=" CB  ASP A  36 "
           model="   0" pdb=" CG  ASP A  36 "
           model="   0" pdb=" OD1 ASP A  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.30   54.30     1      2.00e+01 2.50e-03 9.99e+00
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" CB  ASP A 118 "
           model="   0" pdb=" CG  ASP A 118 "
           model="   0" pdb=" OD1 ASP A 118 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -82.93   52.93     1      2.00e+01 2.50e-03 9.53e+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   83.66  -83.66     1      3.00e+01 1.11e-03 9.49e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 102
       0.029 -    0.058: 53
       0.058 -    0.086: 9
       0.086 -    0.115: 10
       0.115 -    0.143: 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   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-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   -0.11 2.00e-01 2.50e+01 3.24e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 137 "   -0.013 2.00e-02 2.50e+03   8.29e-03 1.38e+00
        model="   0" pdb=" CG  HIS A 137 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 137 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 137 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 137 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 137 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 137 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 137 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.009 2.00e-02 2.50e+03   5.05e-03 7.66e-01
        model="   0" pdb=" CG  TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.013 2.00e-02 2.50e+03   4.97e-03 7.41e-01
        model="   0" pdb=" CG  TYR A  81 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 152
        2.21 -     2.81: 4632
        2.81 -     3.40: 5651
        3.40 -     4.00: 7203
        4.00 -     4.60: 10842
  Nonbonded interactions: 28480
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ILE A  78 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.612 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.793 2.270
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.821 1.850
  nonbonded model="   0" pdb="HD12 ILE A  37 "
            model="   0" pdb="HD23 LEU A  61 "
     model   vdw
     1.832 2.440
  nonbonded model="   0" pdb=" O   VAL A  41 "
            model="   0" pdb=" H   LYS A 113 "
     model   vdw
     1.837 1.850
  ... (remaining 28475 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.73 %
                favored =  94.16 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  13.98
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.53
  MolProbity score      =   2.20

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

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

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

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 463
        1.42 -     1.61: 669
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.269 -0.038 2.00e-02 2.50e+03 3.56e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.334 -0.013 1.00e-02 1.00e+04 1.82e+00
  bond model="   0" pdb=" C   THR A  82 "
       model="   0" pdb=" N   THR A  83 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.74e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.334 -0.013 1.00e-02 1.00e+04 1.68e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.56e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.72 -   106.75: 59
      106.75 -   112.78: 2698
      112.78 -   118.81: 444
      118.81 -   124.84: 835
      124.84 -   130.86: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
        model="   0" pdb=" C   ILE A  86 "
      ideal   model   delta    sigma   weight residual
     111.00  105.92    5.08 2.80e+00 1.28e-01 3.29e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.67    5.33 3.00e+00 1.11e-01 3.16e+00
  angle model="   0" pdb=" 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  103.85    5.15 3.00e+00 1.11e-01 2.95e+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  113.99   -4.99 3.00e+00 1.11e-01 2.77e+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  105.28    4.72 3.00e+00 1.11e-01 2.48e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 990
       16.87 -    33.75: 24
       33.75 -    50.62: 10
       50.62 -    67.50: 4
       67.50 -    84.37: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.49   82.49     1      3.00e+01 1.11e-03 9.27e+00
  dihedral model="   0" pdb=" CA  ASP A  47 "
           model="   0" pdb=" CB  ASP A  47 "
           model="   0" pdb=" CG  ASP A  47 "
           model="   0" pdb=" OD1 ASP A  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -75.58   45.58     1      2.00e+01 2.50e-03 7.20e+00
  dihedral model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
           model="   0" pdb=" CD  GLU A  55 "
           model="   0" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -70.46   70.46     1      3.00e+01 1.11e-03 7.10e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 118
       0.036 -    0.071: 44
       0.071 -    0.106: 9
       0.106 -    0.142: 2
       0.142 -    0.177: 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    2.61   -0.18 2.00e-01 2.50e+01 7.82e-01
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.74e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.012 2.00e-02 2.50e+03   5.07e-03 7.72e-01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.003 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 "    0.002 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 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.014 5.00e-02 4.00e+02   2.14e-02 7.33e-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 "   -0.010 2.00e-02 2.50e+03   4.91e-03 7.23e-01
        model="   0" pdb=" CG  TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 309
        2.29 -     2.86: 5162
        2.86 -     3.44: 5387
        3.44 -     4.02: 7387
        4.02 -     4.60: 10805
  Nonbonded interactions: 29050
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  63 "
            model="   0" pdb=" OD2 ASP A  88 "
     model   vdw
     1.708 1.850
  nonbonded model="   0" pdb="HD13 ILE A  78 "
            model="   0" pdb="HD22 LEU A  99 "
     model   vdw
     1.760 2.440
  nonbonded model="   0" pdb=" H   ILE A  86 "
            model="   0" pdb=" O   TYR A  89 "
     model   vdw
     1.790 1.850
  nonbonded model="   0" pdb=" H   ALA A  48 "
            model="   0" pdb="HH11 ARG A 127 "
     model   vdw
     1.807 2.100
  nonbonded model="   0" pdb=" OE1 GLU A  32 "
            model="   0" pdb="HD21 ASN A  72 "
     model   vdw
     1.834 1.850
  ... (remaining 29045 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.024 (Z=  1.824)
  Mean delta:    0.007 (Z=  0.378)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    5.102 (Z=  2.170)
  Mean delta:    0.999 (Z=  0.519)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   159.54    20.46  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.006
  Max. delta:   87.327
  Mean delta:   15.560

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.149
  Mean delta:    0.052

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.020
  Mean delta:    0.005

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


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

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

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

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 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      :  0.005   0.024   2242  Z= 0.270
    Angle     :  1.221   5.138   4079  Z= 0.475
    Chirality :  0.052   0.149    176
    Planarity :  0.004   0.017    327
    Dihedral  : 12.989  87.327    769
    Min Nonbonded Distance : 1.334
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  2.19 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  2.42 %
      Favored  : 96.77 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.05 (0.72), residues: 137
    helix:  0.32 (0.62), residues: 69
    sheet:  None (None), residues: 0
    loop : -0.14 (0.80), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.017   0.003   PHE A  45 
   TYR   0.029   0.003   TYR A  12 
   ARG   0.016   0.004   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.010   0.003   PHE A  45 
   TYR   0.023   0.004   TYR A  12 
   ARG   0.001   0.000   ARG A  21 

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

   A  43  HIS
   A 137  HIS

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

  Ramachandran outliers =   2.19 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0051
  RMS(angles)           =   1.22
  MolProbity score      =   1.56

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

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

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.89 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 110
        1.23 -     1.43: 362
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.02e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.50e+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 7.14e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 5.99e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.91e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.08 -   106.64: 153
      106.64 -   112.19: 2508
      112.19 -   117.75: 419
      117.75 -   123.31: 815
      123.31 -   128.86: 184
  Bond angle restraints: 4079
  Sorted by residual:
  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  116.33   -3.73 1.00e+00 1.00e+00 1.39e+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  118.88    3.72 1.00e+00 1.00e+00 1.38e+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 1.24e+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=" 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  126.67    4.53 1.30e+00 5.92e-01 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 967
       17.76 -    35.52: 49
       35.52 -    53.28: 10
       53.28 -    71.04: 5
       71.04 -    88.80: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  85 "
           model="   0" pdb=" C   LYS A  85 "
           model="   0" pdb=" N   ILE A  86 "
           model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.95   27.05     0      5.00e+00 4.00e-02 2.93e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.84   23.16     0      5.00e+00 4.00e-02 2.15e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.15   17.85     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 67
       0.039 -    0.077: 46
       0.077 -    0.116: 35
       0.116 -    0.154: 21
       0.154 -    0.193: 7
  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 9.29e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.15e-01
  chirality model="   0" pdb=" CA  LEU A 119 "
            model="   0" pdb=" N   LEU A 119 "
            model="   0" pdb=" C   LEU A 119 "
            model="   0" pdb=" CB  LEU A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.74e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.065 2.00e-02 2.50e+03   2.81e-02 2.37e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 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 "   -0.004 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 "    0.021 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 "    0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.023 2.00e-02 2.50e+03   4.69e-02 2.20e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.081 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.066 2.00e-02 2.50e+03   2.60e-02 2.03e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 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 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     1.96: 23
        1.96 -     2.62: 2526
        2.62 -     3.28: 6784
        3.28 -     3.94: 7818
        3.94 -     4.60: 11783
  Nonbonded interactions: 28934
  Sorted by model distance:
  nonbonded model="   0" pdb="HD21 LEU A  39 "
            model="   0" pdb=" HG3 GLU A 123 "
     model   vdw
     1.303 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.621 1.850
  nonbonded model="   0" pdb="HG21 VAL A  14 "
            model="   0" pdb="HG23 ILE A  86 "
     model   vdw
     1.701 2.440
  nonbonded model="   0" pdb=" HB3 SER A  17 "
            model="   0" pdb="HG21 ILE A  77 "
     model   vdw
     1.726 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.732 1.850
  ... (remaining 28929 not shown)

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

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.92
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.04 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: 78
        1.23 -     1.43: 394
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.11e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.69e+00
  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 6.57e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.49e+00
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.44e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.06 -   105.89: 74
      105.89 -   111.71: 2490
      111.71 -   117.54: 509
      117.54 -   123.37: 833
      123.37 -   129.20: 173
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  128.77   -7.07 1.80e+00 3.09e-01 1.54e+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  128.71   -7.01 1.80e+00 3.09e-01 1.52e+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  126.48    4.72 1.30e+00 5.92e-01 1.32e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.03    3.57 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  126.67    4.53 1.30e+00 5.92e-01 1.21e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 976
       17.32 -    34.65: 37
       34.65 -    51.97: 13
       51.97 -    69.29: 6
       69.29 -    86.61: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.73   19.27     0      5.00e+00 4.00e-02 1.48e+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  160.89   19.11     0      5.00e+00 4.00e-02 1.46e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.03   17.97     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 78
       0.041 -    0.081: 44
       0.081 -    0.121: 33
       0.121 -    0.162: 18
       0.162 -    0.202: 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 1.02e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.49e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.17e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.062 2.00e-02 2.50e+03   2.50e-02 1.88e+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 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.058 2.00e-02 2.50e+03   2.50e-02 1.88e+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 "    0.009 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 "   -0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 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   1.73e-02 8.95e+00
        model="   0" pdb=" CG  TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.027 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 "    0.012 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 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.16: 123
        2.16 -     2.77: 4092
        2.77 -     3.38: 6089
        3.38 -     3.99: 7438
        3.99 -     4.60: 11139
  Nonbonded interactions: 28881
  Sorted by model distance:
  nonbonded model="   0" pdb=" HG1 THR A  82 "
            model="   0" pdb=" O   ASP A  88 "
     model   vdw
     1.555 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.657 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.745 1.850
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.753 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.754 1.850
  ... (remaining 28876 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 0.74, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.557, 69.57, 54.744, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.021 (Z=  1.522)
  Mean delta:    0.004 (Z=  0.218)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.332 (Z=  1.726)
  Mean delta:    0.739 (Z=  0.345)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.014
  Max. delta:   82.207
  Mean delta:   10.885

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.139
  Mean delta:    0.040

                       ----------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   0.021   2242  Z= 0.156
    Angle     :  1.085   4.944   4079  Z= 0.391
    Chirality :  0.040   0.139    176
    Planarity :  0.002   0.025    327
    Dihedral  : 10.114  82.207    769
    Min Nonbonded Distance : 1.680
  
  Molprobity Statistics.
    All-atom Clashscore : 7.21
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  1.61 %
      Favored  : 98.39 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  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 (0.72), residues: 137
    helix:  0.52 (0.60), residues: 64
    sheet:  None (None), residues: 0
    loop :  0.51 (0.80), residues: 73
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.009   0.002   PHE A  45 
   TYR   0.010   0.002   TYR A 111 
   ARG   0.006   0.002   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.004   0.001   PHE A  45 
   TYR   0.009   0.002   TYR A 111 
   ARG   0.003   0.001   ARG A 129 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  3.008)
  Mean delta:    0.012 (Z=  0.632)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.560 (Z=  4.130)
  Mean delta:    1.669 (Z=  0.895)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   152.81    27.19  5.00e+00  2.96e+01   5.4*sigma
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N
   A  81  TYR  CA        180.00   156.96    23.04  5.00e+00  2.12e+01   4.6*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   158.06    21.94  5.00e+00  1.92e+01   4.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   158.44    21.56  5.00e+00  1.86e+01   4.3*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -158.47   -21.53  5.00e+00  1.85e+01   4.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   159.87    20.13  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.008
  Max. delta:   86.132
  Mean delta:   13.331

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.200
  Mean delta:    0.079

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.102       0.173      207.21   8.6*sigma

  Min. delta:    0.000
  Max. delta:    0.102
  Mean delta:    0.014

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.450
    Angle     :  1.585   7.560   4079  Z= 0.682
    Chirality :  0.079   0.200    176
    Planarity :  0.010   0.098    327
    Dihedral  : 11.701  86.132    769
    Min Nonbonded Distance : 1.503
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  :  6.57 %
      Favored  : 87.59 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.10 (0.66), residues: 137
    helix: -0.27 (0.50), residues: 79
    sheet:  None (None), residues: 0
    loop : -1.27 (0.85), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.013   0.003   PHE A  67 
   TYR   0.213   0.018   TYR A  81 
   ARG   0.057   0.014   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.173   0.021   TYR A  81 
   ARG   0.007   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.21
  RMS(bonds)            =   0.0026
  RMS(angles)           =   1.08
  MolProbity score      =   1.56

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.045 (Z=  3.200)
  Mean delta:    0.012 (Z=  0.627)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.004 (Z=  0.002)
  Max. delta:    6.962 (Z=  4.145)
  Mean delta:    1.616 (Z=  0.888)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.048
  Max. delta:   86.651
  Mean delta:   12.720

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.208
  Mean delta:    0.078

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.105       0.179      219.89   8.9*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.052       0.096       54.13   4.8*sigma
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.089       0.092      139.00   4.6*sigma

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

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


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

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

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

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

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

    0" pdbres="HIS A  43  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   0.045   2242  Z= 0.447
    Angle     :  1.548   6.962   4079  Z= 0.674
    Chirality :  0.078   0.208    176
    Planarity :  0.012   0.103    327
    Dihedral  : 11.529  86.651    769
    Min Nonbonded Distance : 1.501
  
  Molprobity Statistics.
    All-atom Clashscore : 14.43
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  4.38 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  7.26 %
      Favored  : 91.13 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.16 (0.68), residues: 137
    helix: -0.13 (0.49), residues: 86
    sheet:  None (None), residues: 0
    loop :  0.26 (0.95), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.215   0.027   PHE A  15 
   TYR   0.221   0.021   TYR A  91 
   ARG   0.037   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.141   0.029   PHE A  15 
   TYR   0.179   0.025   TYR A  91 
   ARG   0.005   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   5.84 %
                favored =  87.59 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.59
  MolProbity score      =   2.29

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  94.16 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  14.43
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.55
  MolProbity score      =   2.22

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

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


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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.79 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: 389
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.80e+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 6.83e+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 6.69e+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 6.48e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.43e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.13 -   105.88: 77
      105.88 -   111.63: 2457
      111.63 -   117.37: 521
      117.37 -   123.12: 808
      123.12 -   128.87: 216
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.58    4.02 1.00e+00 1.00e+00 1.61e+01
  angle model="   0" pdb=" 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  116.19   -3.59 1.00e+00 1.00e+00 1.29e+01
  angle model="   0" pdb=" C   THR A  82 "
        model="   0" pdb=" N   THR A  83 "
        model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  127.87   -6.17 1.80e+00 3.09e-01 1.17e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.01   -3.41 1.00e+00 1.00e+00 1.17e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.20    3.40 1.00e+00 1.00e+00 1.15e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.25: 961
       16.25 -    32.50: 51
       32.50 -    48.76: 15
       48.76 -    65.01: 5
       65.01 -    81.26: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.77   23.23     0      5.00e+00 4.00e-02 2.16e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.02   17.98     0      5.00e+00 4.00e-02 1.29e+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  164.94   15.06     0      5.00e+00 4.00e-02 9.08e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.042: 77
       0.042 -    0.083: 43
       0.083 -    0.125: 32
       0.125 -    0.166: 21
       0.166 -    0.208: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.08e+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 9.61e-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 8.67e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.182 2.00e-02 2.50e+03   7.56e-02 1.72e+02
        model="   0" pdb=" CG  TYR A  89 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.142 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.036 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.130 2.00e-02 2.50e+03   5.42e-02 8.83e+01
        model="   0" pdb=" CG  TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.099 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.059 2.00e-02 2.50e+03   2.55e-02 1.95e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.051 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 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.015 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 152
        2.20 -     2.80: 4343
        2.80 -     3.40: 5995
        3.40 -     4.00: 7253
        4.00 -     4.60: 11020
  Nonbonded interactions: 28763
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 ASP A  74 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.596 2.440
  nonbonded model="   0" pdb=" HE2 TYR A  91 "
            model="   0" pdb="HD23 LEU A  99 "
     model   vdw
     1.639 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.656 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.662 1.850
  nonbonded model="   0" pdb=" HZ  PHE A  67 "
            model="   0" pdb=" HB3 TYR A  89 "
     model   vdw
     1.678 2.270
  ... (remaining 28758 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.835)
  Mean delta:    0.012 (Z=  0.621)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.856 (Z=  3.803)
  Mean delta:    1.612 (Z=  0.873)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   146.37    33.63  5.00e+00  4.52e+01   6.7*sigma

  Min. delta:    0.006
  Max. delta:   82.103
  Mean delta:   12.421

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.205
  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      :  0.008   0.039   2242  Z= 0.443
    Angle     :  1.549   6.856   4079  Z= 0.667
    Chirality :  0.077   0.205    176
    Planarity :  0.008   0.042    327
    Dihedral  : 11.372  82.103    769
    Min Nonbonded Distance : 1.569
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    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 : 0.76 %
  
  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:  0.38 (0.69), residues: 137
    helix:  0.10 (0.52), residues: 82
    sheet: -2.74 (1.15), residues: 12
    loop :  2.06 (0.99), residues: 43
  
  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   0.063   0.009   TYR A 111 
   ARG   0.039   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.008   0.003   PHE A  67 
   TYR   0.053   0.011   TYR A 111 
   ARG   0.005   0.001   ARG A  21 

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

   A  66  GLN

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.042 (Z=  2.633)
  Mean delta:    0.012 (Z=  0.631)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   116.75    -4.15  1.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.550 (Z=  4.148)
  Mean delta:    1.620 (Z=  0.889)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -156.39   -23.61  5.00e+00  2.23e+01   4.7*sigma

  Min. delta:    0.002
  Max. delta:   67.373
  Mean delta:   12.442

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.210
  Mean delta:    0.080

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.091
  Mean delta:    0.014

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


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

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

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

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

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

    0" pdbres="HIS A  43  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   2242  Z= 0.449
    Angle     :  1.554   6.550   4079  Z= 0.676
    Chirality :  0.080   0.210    176
    Planarity :  0.010   0.083    327
    Dihedral  : 11.182  67.373    769
    Min Nonbonded Distance : 1.438
  
  Molprobity Statistics.
    All-atom Clashscore : 14.43
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.84 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  2.42 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.16 (0.71), residues: 137
    helix:  0.57 (0.53), residues: 84
    sheet:  None (None), residues: 0
    loop : -1.13 (0.93), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 136 
   PHE   0.100   0.014   PHE A  15 
   TYR   0.209   0.021   TYR A  81 
   ARG   0.040   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 136 
   PHE   0.065   0.014   PHE A  15 
   TYR   0.172   0.025   TYR A  81 
   ARG   0.003   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.852)
  Mean delta:    0.012 (Z=  0.657)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.875 (Z=  4.219)
  Mean delta:    1.656 (Z=  0.889)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   135.56    44.44  5.00e+00  7.90e+01   8.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   141.60    38.40  5.00e+00  5.90e+01   7.7*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   149.78    30.22  5.00e+00  3.65e+01   6.0*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   153.18    26.82  5.00e+00  2.88e+01   5.4*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -159.53   -20.47  5.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.003
  Max. delta:   85.232
  Mean delta:   13.246

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.231
  Mean delta:    0.080

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.074
  Mean delta:    0.012

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.581   8.875   4079  Z= 0.679
    Chirality :  0.080   0.231    176
    Planarity :  0.009   0.056    327
    Dihedral  : 11.587  85.232    769
    Min Nonbonded Distance : 1.730
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  :  4.38 %
      Favored  : 89.05 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.84 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.39 (0.69), residues: 137
    helix:  0.28 (0.51), residues: 89
    sheet:  None (None), residues: 0
    loop : -1.15 (0.96), residues: 48
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.015   0.003   PHE A  67 
   TYR   0.073   0.009   TYR A  50 
   ARG   0.060   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.015   0.004   PHE A  67 
   TYR   0.059   0.010   TYR A  50 
   ARG   0.007   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.55
  MolProbity score      =   1.35

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  94.16 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =  14.43
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.55
  MolProbity score      =   2.35

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

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

  Ramachandran outliers =   6.57 %
                favored =  89.05 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.58
  MolProbity score      =   1.92

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.026 (Z=  1.838)
  Mean delta:    0.004 (Z=  0.274)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.767 (Z=  1.369)
  Mean delta:    0.723 (Z=  0.344)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   86.353
  Mean delta:   12.275

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.135
  Mean delta:    0.040

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.026   2242  Z= 0.195
    Angle     :  1.083   5.206   4079  Z= 0.391
    Chirality :  0.040   0.135    176
    Planarity :  0.002   0.023    327
    Dihedral  : 11.583  86.353    769
    Min Nonbonded Distance : 1.599
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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:  0.59 (0.71), residues: 137
    helix:  0.26 (0.59), residues: 71
    sheet:  None (None), residues: 0
    loop :  0.80 (0.81), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.005   0.002   PHE A  15 
   TYR   0.019   0.003   TYR A  91 
   ARG   0.015   0.003   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.015   0.003   TYR A  91 
   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)----------                  

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0032
  RMS(angles)           =   1.08
  MolProbity score      =   1.71

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.128)
  Mean delta:    0.012 (Z=  0.646)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.465 (Z=  4.176)
  Mean delta:    1.625 (Z=  0.886)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   158.44    21.56  5.00e+00  1.86e+01   4.3*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   159.58    20.42  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.018
  Max. delta:   87.685
  Mean delta:   12.755

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.219
  Mean delta:    0.082

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.080
  Mean delta:    0.012

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.460
    Angle     :  1.555   6.685   4079  Z= 0.674
    Chirality :  0.082   0.219    176
    Planarity :  0.009   0.060    327
    Dihedral  : 11.714  87.685    769
    Min Nonbonded Distance : 1.440
  
  Molprobity Statistics.
    All-atom Clashscore : 14.88
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.84 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  5.65 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.72 (0.67), residues: 137
    helix:  0.07 (0.52), residues: 82
    sheet:  None (None), residues: 0
    loop : -1.22 (0.83), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.017   0.004   PHE A  45 
   TYR   0.066   0.008   TYR A  50 
   ARG   0.065   0.015   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.054   0.010   TYR A  50 
   ARG   0.007   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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


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


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

  Ramachandran outliers =   2.19 %
                favored =  91.97 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  14.88
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.56
  MolProbity score      =   2.17

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.021 (Z=  1.509)
  Mean delta:    0.004 (Z=  0.210)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.744 (Z=  1.421)
  Mean delta:    0.711 (Z=  0.344)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.009
  Max. delta:   73.956
  Mean delta:    9.906

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.138
  Mean delta:    0.036

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.021   2242  Z= 0.150
    Angle     :  1.071   5.128   4079  Z= 0.388
    Chirality :  0.036   0.138    176
    Planarity :  0.002   0.023    327
    Dihedral  :  9.897  80.048    769
    Min Nonbonded Distance : 1.633
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.58 (0.72), residues: 137
    helix: -0.45 (0.56), residues: 73
    sheet:  None (None), residues: 0
    loop :  1.80 (0.85), residues: 64
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.006   0.002   PHE A  15 
   TYR   0.009   0.002   TYR A  81 
   ARG   0.010   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.009   0.002   TYR A  81 
   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)----------                  

  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0025
  RMS(angles)           =   1.07
  MolProbity score      =   1.57

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  1.386)
  Mean delta:    0.004 (Z=  0.246)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.059 (Z=  1.353)
  Mean delta:    0.564 (Z=  0.286)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   86.443
  Mean delta:   14.472

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.157
  Mean delta:    0.041

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.014
  Mean delta:    0.002

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


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

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

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

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 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   2242  Z= 0.176
    Angle     :  1.034   4.947   4079  Z= 0.369
    Chirality :  0.041   0.157    176
    Planarity :  0.002   0.014    327
    Dihedral  : 12.154  86.443    769
    Min Nonbonded Distance : 1.613
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  1.61 %
      Favored  : 98.39 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.95 (0.62), residues: 137
    helix: -0.19 (0.56), residues: 73
    sheet:  None (None), residues: 0
    loop : -1.07 (0.63), residues: 64
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.006   0.001   PHE A  45 
   TYR   0.009   0.002   TYR A  12 
   ARG   0.005   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.005   0.001   PHE A  45 
   TYR   0.007   0.002   TYR A 111 
   ARG   0.001   0.000   ARG A  21 

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

   A  43  HIS
   A  66  GLN

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.662)
  Mean delta:    0.012 (Z=  0.610)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.505 (Z=  3.989)
  Mean delta:    1.631 (Z=  0.879)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   148.80    31.20  5.00e+00  3.89e+01   6.2*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   155.06    24.94  5.00e+00  2.49e+01   5.0*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   155.64    24.36  5.00e+00  2.37e+01   4.9*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   157.77    22.23  5.00e+00  1.98e+01   4.4*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   158.11    21.89  5.00e+00  1.92e+01   4.4*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -158.49   -21.51  5.00e+00  1.85e+01   4.3*sigma

  Min. delta:    0.041
  Max. delta:   87.872
  Mean delta:   12.770

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.246
  Mean delta:    0.080

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.043
  Mean delta:    0.011

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.434
    Angle     :  1.566   7.146   4079  Z= 0.673
    Chirality :  0.080   0.246    176
    Planarity :  0.008   0.042    327
    Dihedral  : 12.039  87.872    769
    Min Nonbonded Distance : 1.589
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  8.03 %
      Favored  : 89.05 %
    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 : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.84 (0.67), residues: 137
    helix: -0.64 (0.55), residues: 75
    sheet:  None (None), residues: 0
    loop : -1.91 (0.78), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 134 
   PHE   0.015   0.004   PHE A  67 
   TYR   0.073   0.010   TYR A  50 
   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 134 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.061   0.012   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  3.013)
  Mean delta:    0.012 (Z=  0.634)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.986 (Z=  3.749)
  Mean delta:    1.591 (Z=  0.868)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   151.70    28.30  5.00e+00  3.20e+01   5.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   153.46    26.54  5.00e+00  2.82e+01   5.3*sigma

  Min. delta:    0.027
  Max. delta:   89.236
  Mean delta:   12.009

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.210
  Mean delta:    0.072

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.056
  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   2242  Z= 0.452
    Angle     :  1.535   6.986   4079  Z= 0.664
    Chirality :  0.072   0.210    176
    Planarity :  0.008   0.042    327
    Dihedral  : 11.193  89.236    769
    Min Nonbonded Distance : 1.352
  
  Molprobity Statistics.
    All-atom Clashscore : 21.19
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  5.11 %
      Favored  : 91.97 %
    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: -0.32 (0.67), residues: 137
    helix:  0.28 (0.52), residues: 85
    sheet:  None (None), residues: 0
    loop : -0.89 (0.85), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.084   0.013   PHE A  15 
   TYR   0.048   0.008   TYR A  91 
   ARG   0.044   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.054   0.014   PHE A  15 
   TYR   0.039   0.010   TYR A  91 
   ARG   0.006   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.03
  MolProbity score      =   1.19

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.92 %
                favored =  89.05 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.57
  MolProbity score      =   2.02

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.92 %
                favored =  91.97 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  21.19
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.54
  MolProbity score      =   2.47

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.024 (Z=  1.709)
  Mean delta:    0.005 (Z=  0.264)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.863 (Z=  1.520)
  Mean delta:    0.604 (Z=  0.307)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   89.305
  Mean delta:   16.927

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.136
  Mean delta:    0.040

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.008
  Mean delta:    0.002

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.024   2242  Z= 0.189
    Angle     :  1.047   4.864   4079  Z= 0.377
    Chirality :  0.040   0.136    176
    Planarity :  0.002   0.008    327
    Dihedral  : 14.340  89.305    769
    Min Nonbonded Distance : 1.433
  
  Molprobity Statistics.
    All-atom Clashscore : 16.23
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.84 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  1.61 %
      Favored  : 96.77 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.89 (0.67), residues: 137
    helix: -0.75 (0.53), residues: 71
    sheet:  None (None), residues: 0
    loop : -0.20 (0.79), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 136 
   PHE   0.005   0.002   PHE A  67 
   TYR   0.011   0.002   TYR A  12 
   ARG   0.006   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 136 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.008   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 ===================================


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.908)
  Mean delta:    0.012 (Z=  0.640)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   116.79    -4.19  1.00e+00  1.76e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.60     4.00  1.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    8.084 (Z=  4.191)
  Mean delta:    1.692 (Z=  0.891)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   146.93    33.07  5.00e+00  4.38e+01   6.6*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   149.11    30.89  5.00e+00  3.82e+01   6.2*sigma
   A 125  LYS  CA
   A 125  LYS  C
   A 126  VAL  N
   A 126  VAL  CA        180.00   153.78    26.22  5.00e+00  2.75e+01   5.2*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   155.78    24.22  5.00e+00  2.35e+01   4.8*sigma
   A 124  ALA  CA
   A 124  ALA  C
   A 125  LYS  N
   A 125  LYS  CA        180.00   156.80    23.20  5.00e+00  2.15e+01   4.6*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   157.47    22.53  5.00e+00  2.03e+01   4.5*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   157.94    22.06  5.00e+00  1.95e+01   4.4*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00   158.10    21.90  5.00e+00  1.92e+01   4.4*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   158.65    21.35  5.00e+00  1.82e+01   4.3*sigma
   A 126  VAL  CA
   A 126  VAL  C
   A 127  ARG  N
   A 127  ARG  CA        180.00   159.93    20.07  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.007
  Max. delta:   83.934
  Mean delta:   12.347

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.191
  Mean delta:    0.078

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.456
    Angle     :  1.594   8.084   4079  Z= 0.679
    Chirality :  0.078   0.191    176
    Planarity :  0.008   0.037    327
    Dihedral  : 10.792  83.934    769
    Min Nonbonded Distance : 1.515
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  8.03 %
      Allowed  :  5.11 %
      Favored  : 86.86 %
    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 : 1.53 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -2.10 (0.65), residues: 137
    helix: -1.11 (0.52), residues: 76
    sheet: -1.33 (1.11), residues: 12
    loop : -1.62 (0.92), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.010   0.003   PHE A  45 
   TYR   0.063   0.011   TYR A 111 
   ARG   0.039   0.008   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.006   0.002   PHE A  67 
   TYR   0.053   0.013   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.73 %
                favored =  93.43 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  16.23
  RMS(bonds)            =   0.0032
  RMS(angles)           =   1.05
  MolProbity score      =   2.30

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   8.03 %
                favored =  86.86 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.59
  MolProbity score      =   1.94

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: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

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


End of input processing

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

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  1.363)
  Mean delta:    0.004 (Z=  0.231)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.030 (Z=  1.515)
  Mean delta:    0.690 (Z=  0.315)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   82.428
  Mean delta:   11.212

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.152
  Mean delta:    0.045

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.021   2242  Z= 0.165
    Angle     :  1.079   4.957   4079  Z= 0.383
    Chirality :  0.045   0.152    176
    Planarity :  0.002   0.023    327
    Dihedral  : 10.717  82.428    769
    Min Nonbonded Distance : 1.658
  
  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:  0.61 (0.69), residues: 137
    helix: -0.13 (0.63), residues: 68
    sheet:  2.18 (1.77), residues: 10
    loop :  1.05 (0.72), residues: 59
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.005   0.001   PHE A  45 
   TYR   0.011   0.003   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.010   0.003   TYR A 111 
   ARG   0.002   0.000   ARG A 129 

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

  No backwards Asn/Gln/His sidechains found.

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


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


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A 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 ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.00 %
                favored = 100.00 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   4.51
  RMS(bonds)            =   0.0027
  RMS(angles)           =   1.08
  MolProbity score      =   1.23

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

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


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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.425)
  Mean delta:    0.012 (Z=  0.628)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.166 (Z=  3.778)
  Mean delta:    1.570 (Z=  0.850)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   159.39    20.61  5.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.000
  Max. delta:   89.964
  Mean delta:   13.558

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.270
  Mean delta:    0.079

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.054
  Mean delta:    0.012

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.447
    Angle     :  1.522   7.166   4079  Z= 0.653
    Chirality :  0.079   0.270    176
    Planarity :  0.009   0.045    327
    Dihedral  : 11.765  89.964    769
    Min Nonbonded Distance : 1.590
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  0.81 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.29 (0.67), residues: 137
    helix:  0.14 (0.50), residues: 84
    sheet:  None (None), residues: 0
    loop : -0.54 (0.90), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.017   0.005   PHE A  15 
   TYR   0.072   0.009   TYR A  50 
   ARG   0.044   0.011   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.012   0.005   PHE A  67 
   TYR   0.060   0.011   TYR A  50 
   ARG   0.005   0.001   ARG A  21 

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

   A 100  GLN

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

  Time building chain proxies: 1.04, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.125, 81.592, 42.005, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.037 (Z=  2.680)
  Mean delta:    0.012 (Z=  0.627)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.60     4.00  1.00e+00  1.60e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.103 (Z=  4.003)
  Mean delta:    1.684 (Z=  0.915)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -153.12   -26.88  5.00e+00  2.89e+01   5.4*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00   155.42    24.58  5.00e+00  2.42e+01   4.9*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   157.25    22.75  5.00e+00  2.07e+01   4.6*sigma
   A 113  LYS  CA
   A 113  LYS  C
   A 114  PRO  N
   A 114  PRO  CA        180.00   159.81    20.19  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.062
  Max. delta:   87.340
  Mean delta:   13.893

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.186
  Mean delta:    0.076

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.074
  Mean delta:    0.012

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.037   2242  Z= 0.446
    Angle     :  1.588   8.085   4079  Z= 0.691
    Chirality :  0.076   0.186    176
    Planarity :  0.009   0.056    327
    Dihedral  : 11.815  87.340    769
    Min Nonbonded Distance : 1.685
  
  Molprobity Statistics.
    All-atom Clashscore : 0.90
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  : 10.95 %
      Favored  : 86.13 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.03 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.81 (0.66), residues: 137
    helix: -0.43 (0.50), residues: 82
    sheet:  None (None), residues: 0
    loop : -2.37 (0.83), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A  43 
   PHE   0.014   0.003   PHE A  67 
   TYR   0.060   0.010   TYR A 111 
   ARG   0.061   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A  43 
   PHE   0.013   0.003   PHE A  67 
   TYR   0.050   0.012   TYR A 111 
   ARG   0.006   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


End of input processing

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

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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:    0.027 (Z=  1.479)
  Mean delta:    0.004 (Z=  0.259)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.738 (Z=  1.634)
  Mean delta:    0.730 (Z=  0.340)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   88.670
  Mean delta:   11.899

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.164
  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   0.027   2242  Z= 0.185
    Angle     :  1.117   5.178   4079  Z= 0.400
    Chirality :  0.042   0.164    176
    Planarity :  0.002   0.026    327
    Dihedral  : 10.845  88.670    769
    Min Nonbonded Distance : 1.451
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.73 %
      Favored  : 99.27 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.80 (0.69), residues: 137
    helix:  0.22 (0.57), residues: 79
    sheet:  None (None), residues: 0
    loop :  1.33 (0.80), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.004   0.001   PHE A  45 
   TYR   0.012   0.003   TYR A  91 
   ARG   0.005   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.009   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A  58 

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

   A  66  GLN

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

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

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

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

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

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.52
  MolProbity score      =   1.82

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.92 %
                favored =  86.13 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   0.90
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.59
  MolProbity score      =   1.70

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            =   8.57
  RMS(bonds)            =   0.0031
  RMS(angles)           =   1.12
  MolProbity score      =   1.46

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

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


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


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

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (48.353, 40.936, 71.949, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.183)
  Mean delta:    0.012 (Z=  0.610)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.793 (Z=  4.197)
  Mean delta:    1.546 (Z=  0.850)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   81.734
  Mean delta:   12.151

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.196
  Mean delta:    0.076

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  36  ASP  CB
   A  36  ASP  CG
   A  36  ASP  OD1
   A  36  ASP  OD2           0.050       0.087       25.25   4.3*sigma

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.434
    Angle     :  1.507   6.793   4079  Z= 0.652
    Chirality :  0.076   0.196    176
    Planarity :  0.008   0.050    327
    Dihedral  : 11.143  81.734    769
    Min Nonbonded Distance : 1.380
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  1.46 %
      Favored  : 97.81 %
    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:  0.16 (0.69), residues: 137
    helix:  0.50 (0.52), residues: 85
    sheet:  None (None), residues: 0
    loop : -0.39 (0.91), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.039   0.008   PHE A  15 
   TYR   0.069   0.009   TYR A  50 
   ARG   0.034   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.024   0.008   PHE A  15 
   TYR   0.057   0.011   TYR A  50 
   ARG   0.004   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
  Ramachandran outliers =   0.73 %
                favored =  97.81 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.51
  MolProbity score      =   1.64

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.722)
  Mean delta:    0.012 (Z=  0.614)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.342 (Z=  3.914)
  Mean delta:    1.604 (Z=  0.873)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   156.19    23.81  5.00e+00  2.27e+01   4.8*sigma

  Min. delta:    0.022
  Max. delta:   75.282
  Mean delta:   12.359

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.201
  Mean delta:    0.076

                       ----------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      :  0.008   0.041   2242  Z= 0.437
    Angle     :  1.544   6.342   4079  Z= 0.667
    Chirality :  0.076   0.201    176
    Planarity :  0.008   0.044    327
    Dihedral  : 11.346  80.022    769
    Min Nonbonded Distance : 1.557
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  6.57 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  2.42 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.51 (0.72), residues: 137
    helix:  0.22 (0.53), residues: 88
    sheet:  None (None), residues: 0
    loop : -1.23 (1.00), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.001   HIS A 139 
   PHE   0.038   0.007   PHE A  15 
   TYR   0.077   0.011   TYR A  50 
   ARG   0.045   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.001   HIS A 139 
   PHE   0.022   0.007   PHE A  15 
   TYR   0.065   0.013   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.808)
  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   118.32     4.28  1.00e+00  1.83e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.654 (Z=  4.280)
  Mean delta:    1.604 (Z=  0.884)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00  -158.46   -21.54  5.00e+00  1.86e+01   4.3*sigma

  Min. delta:    0.002
  Max. delta:   85.121
  Mean delta:   12.783

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.214
  Mean delta:    0.077

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.045
  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   0.038   2242  Z= 0.456
    Angle     :  1.541   6.654   4079  Z= 0.671
    Chirality :  0.077   0.214    176
    Planarity :  0.008   0.041    327
    Dihedral  : 11.445  85.121    769
    Min Nonbonded Distance : 1.594
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.03 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.16 (0.68), residues: 137
    helix:  0.44 (0.52), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.80 (0.87), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.020   0.005   PHE A  67 
   TYR   0.076   0.011   TYR A  81 
   ARG   0.039   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.061   0.013   TYR A  81 
   ARG   0.005   0.001   ARG A  21 

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

   A  66  GLN

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


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


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

  Ramachandran outliers =   2.19 %
                favored =  91.24 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.54
  MolProbity score      =   2.10

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.23, per 1000 atoms: 0.55
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.539, 63.016, 46.823, 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     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.54
  MolProbity score      =   1.78

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.019 (Z=  1.434)
  Mean delta:    0.004 (Z=  0.241)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.838 (Z=  1.613)
  Mean delta:    0.599 (Z=  0.298)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.004
  Max. delta:   83.252
  Mean delta:   11.579

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.148
  Mean delta:    0.040

                       ----------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   0.019   2242  Z= 0.172
    Angle     :  1.047   4.838   4079  Z= 0.375
    Chirality :  0.040   0.148    176
    Planarity :  0.002   0.021    327
    Dihedral  : 11.182  83.252    769
    Min Nonbonded Distance : 1.389
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.23 (0.66), residues: 137
    helix: -0.46 (0.56), residues: 68
    sheet:  None (None), residues: 0
    loop :  0.39 (0.73), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.005   0.002   PHE A  15 
   TYR   0.015   0.002   TYR A  12 
   ARG   0.005   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.011   0.002   TYR A  12 
   ARG   0.001   0.000   ARG A 129 

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

   A 100  GLN

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


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

  Time building chain proxies: 0.68, per 1000 atoms: 0.31
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.182, 78.578, 57.797, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0028
  RMS(angles)           =   1.05
  MolProbity score      =   1.61

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

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

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

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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

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


End of input processing

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

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  2.794)
  Mean delta:    0.012 (Z=  0.618)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   129.46    -7.76  1.80e+00  1.86e+01   4.3*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.761 (Z=  4.312)
  Mean delta:    1.593 (Z=  0.869)

                      ----------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   150.03    29.97  5.00e+00  3.59e+01   6.0*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   158.86    21.14  5.00e+00  1.79e+01   4.2*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00  -159.84   -20.16  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.029
  Max. delta:   89.595
  Mean delta:   12.635

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.213
  Mean delta:    0.078

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.081
  Mean delta:    0.013

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.440
    Angle     :  1.545   7.974   4079  Z= 0.666
    Chirality :  0.078   0.213    176
    Planarity :  0.009   0.061    327
    Dihedral  : 11.898  89.595    769
    Min Nonbonded Distance : 1.629
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  3.23 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.12 (0.69), residues: 137
    helix:  0.07 (0.51), residues: 90
    sheet:  None (None), residues: 0
    loop : -0.09 (0.97), residues: 47
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.018   0.005   PHE A  67 
   TYR   0.086   0.015   TYR A  89 
   ARG   0.066   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.069   0.018   TYR A  89 
   ARG   0.006   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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

  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.54
  MolProbity score      =   1.97

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

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


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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 1.19 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)----------                  


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.622)
  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:    7.079 (Z=  3.905)
  Mean delta:    1.641 (Z=  0.895)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   85.681
  Mean delta:   13.181

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.211
  Mean delta:    0.081

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.068
  Mean delta:    0.012

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.471
    Angle     :  1.570   7.079   4079  Z= 0.681
    Chirality :  0.081   0.211    176
    Planarity :  0.009   0.051    327
    Dihedral  : 11.587  85.681    769
    Min Nonbonded Distance : 0.969
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  3.23 %
      Favored  : 91.94 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.33 (0.69), residues: 137
    helix:  0.15 (0.51), residues: 90
    sheet:  None (None), residues: 0
    loop : -0.71 (0.95), residues: 47
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.014   0.004   PHE A  45 
   TYR   0.069   0.010   TYR A  50 
   ARG   0.056   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.058   0.012   TYR A  50 
   ARG   0.006   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 87
        1.23 -     1.43: 385
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.22e+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 6.19e+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 6.18e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.05e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.76e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.53 -   106.21: 105
      106.21 -   111.89: 2494
      111.89 -   117.58: 472
      117.58 -   123.26: 820
      123.26 -   128.94: 188
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.76    3.84 1.00e+00 1.00e+00 1.48e+01
  angle model="   0" pdb=" 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  126.21    4.99 1.30e+00 5.92e-01 1.47e+01
  angle model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     121.70  128.49   -6.79 1.80e+00 3.09e-01 1.42e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.09    3.51 1.00e+00 1.00e+00 1.23e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.76    4.44 1.30e+00 5.92e-01 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 963
       17.44 -    34.88: 47
       34.88 -    52.32: 17
       52.32 -    69.75: 2
       69.75 -    87.19: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.74   20.26     0      5.00e+00 4.00e-02 1.64e+01
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.33   18.67     0      5.00e+00 4.00e-02 1.39e+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  161.33   18.67     0      5.00e+00 4.00e-02 1.39e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 67
       0.039 -    0.078: 49
       0.078 -    0.116: 38
       0.116 -    0.155: 18
       0.155 -    0.194: 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 9.40e-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   -2.76    0.17 2.00e-01 2.50e+01 7.33e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.067 2.00e-02 2.50e+03   2.68e-02 2.15e+01
        model="   0" pdb=" CG  TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.056 2.00e-02 2.50e+03   2.47e-02 1.83e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 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 "    0.020 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 "    0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.057 2.00e-02 2.50e+03   2.31e-02 1.60e+01
        model="   0" pdb=" CG  TYR A  89 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.023 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.012 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.29 -     1.95: 19
        1.95 -     2.61: 2412
        2.61 -     3.28: 6745
        3.28 -     3.94: 7761
        3.94 -     4.60: 11798
  Nonbonded interactions: 28735
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LYS A  85 "
            model="   0" pdb=" HH  TYR A  89 "
     model   vdw
     1.291 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.723 1.850
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" HD1 TYR A  91 "
     model   vdw
     1.749 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.755 1.850
  nonbonded model="   0" pdb=" HE  ARG A  21 "
            model="   0" pdb=" OD2 ASP A  29 "
     model   vdw
     1.817 1.850
  ... (remaining 28730 not shown)

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.026 (Z=  1.884)
  Mean delta:    0.004 (Z=  0.252)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.112 (Z=  1.405)
  Mean delta:    0.585 (Z=  0.298)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   83.663
  Mean delta:   14.271

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.143
  Mean delta:    0.041

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.026   2242  Z= 0.180
    Angle     :  1.053   5.078   4079  Z= 0.377
    Chirality :  0.041   0.143    176
    Planarity :  0.002   0.016    327
    Dihedral  : 12.077  83.663    769
    Min Nonbonded Distance : 1.612
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    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: -1.09 (0.66), residues: 137
    helix: -0.45 (0.54), residues: 75
    sheet:  None (None), residues: 0
    loop : -0.94 (0.77), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 137 
   PHE   0.005   0.002   PHE A  15 
   TYR   0.013   0.003   TYR A  81 
   ARG   0.005   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 137 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.010   0.002   TYR A  81 
   ARG   0.002   0.001   ARG A  58 

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

   A 137  HIS
   A  66  GLN

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

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

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

  Ramachandran outliers =   0.00 %
                favored =  94.89 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0088
  RMS(angles)           =   1.57
  MolProbity score      =   2.32

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0031
  RMS(angles)           =   1.05
  MolProbity score      =   1.35

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

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

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

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


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


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

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

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


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

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

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

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.665)
  Mean delta:    0.012 (Z=  0.619)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.762 (Z=  4.176)
  Mean delta:    1.577 (Z=  0.867)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.024
  Max. delta:   85.640
  Mean delta:   12.306

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.175
  Mean delta:    0.075

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

  atoms                 rms_deltas   delta_max    residual   deviation
   A  36  ASP  CB
   A  36  ASP  CG
   A  36  ASP  OD1
   A  36  ASP  OD2           0.047       0.082       22.42   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.053
  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   2242  Z= 0.441
    Angle     :  1.526   6.762   4079  Z= 0.662
    Chirality :  0.075   0.175    176
    Planarity :  0.009   0.047    327
    Dihedral  : 11.663  85.640    769
    Min Nonbonded Distance : 1.264
  
  Molprobity Statistics.
    All-atom Clashscore : 13.98
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    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: -0.85 (0.70), residues: 137
    helix: -0.12 (0.50), residues: 93
    sheet:  None (None), residues: 0
    loop : -1.31 (1.04), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS A 137 
   PHE   0.064   0.009   PHE A  15 
   TYR   0.056   0.012   TYR A 111 
   ARG   0.043   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS A 137 
   PHE   0.042   0.010   PHE A  15 
   TYR   0.047   0.015   TYR A 111 
   ARG   0.005   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.840)
  Mean delta:    0.012 (Z=  0.622)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.086 (Z=  3.610)
  Mean delta:    1.584 (Z=  0.836)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   152.27    27.73  5.00e+00  3.08e+01   5.5*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   152.75    27.25  5.00e+00  2.97e+01   5.4*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   154.93    25.07  5.00e+00  2.51e+01   5.0*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00   155.01    24.99  5.00e+00  2.50e+01   5.0*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   155.07    24.93  5.00e+00  2.49e+01   5.0*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   155.79    24.21  5.00e+00  2.34e+01   4.8*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   155.91    24.09  5.00e+00  2.32e+01   4.8*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   155.97    24.03  5.00e+00  2.31e+01   4.8*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   156.02    23.98  5.00e+00  2.30e+01   4.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   159.80    20.20  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.009
  Max. delta:   89.148
  Mean delta:   12.792

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.199
  Mean delta:    0.072

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

  All restrained atoms within 4.0 sigma of ideal values.

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

============================= 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   2242  Z= 0.443
    Angle     :  1.532   7.086   4079  Z= 0.648
    Chirality :  0.072   0.199    176
    Planarity :  0.007   0.035    327
    Dihedral  : 11.304  89.148    769
    Min Nonbonded Distance : 1.296
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  :  7.30 %
      Favored  : 86.86 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.00 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.82 (0.69), residues: 137
    helix: -1.04 (0.53), residues: 75
    sheet:  None (None), residues: 0
    loop : -1.29 (0.86), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 134 
   PHE   0.015   0.004   PHE A  67 
   TYR   0.058   0.010   TYR A  50 
   ARG   0.040   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 134 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.048   0.012   TYR A  50 
   ARG   0.003   0.000   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Ramachandran outliers =   0.73 %
                favored =  94.16 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  13.98
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.53
  MolProbity score      =   2.20

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: 0.63
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.72 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: 1.25 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: 79
        1.23 -     1.43: 393
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 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 6.85e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.72e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.57e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.37e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.29e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.23 -   105.98: 89
      105.98 -   111.73: 2464
      111.73 -   117.49: 504
      117.49 -   123.24: 830
      123.24 -   128.99: 192
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.65    3.95 1.00e+00 1.00e+00 1.56e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.10    3.50 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" 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  126.71    4.49 1.30e+00 5.92e-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  116.05   -3.45 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.99   -4.59 1.40e+00 5.10e-01 1.08e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 968
       17.47 -    34.94: 52
       34.94 -    52.41: 9
       52.41 -    69.88: 3
       69.88 -    87.35: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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 -157.87  -22.13     0      5.00e+00 4.00e-02 1.96e+01
  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 -161.27  -18.73     0      5.00e+00 4.00e-02 1.40e+01
  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 -162.95  -17.05     0      5.00e+00 4.00e-02 1.16e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.043: 76
       0.043 -    0.086: 50
       0.086 -    0.129: 34
       0.129 -    0.172: 12
       0.172 -    0.214: 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    2.30    0.21 2.00e-01 2.50e+01 1.15e+00
  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    2.31    0.20 2.00e-01 2.50e+01 9.56e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.42e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.074 2.00e-02 2.50e+03   3.26e-02 3.18e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.067 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.052 2.00e-02 2.50e+03   2.08e-02 1.29e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.035 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 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.044 2.00e-02 2.50e+03   1.66e-02 8.28e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.010 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 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.022 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 "   -0.011 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 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 211
        2.25 -     2.84: 471
  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
1
        2.84 -     3.42: 5721
        3.42 -     4.01: 7071
        4.01 -     4.60: 10479
  Nonbonded interactions: 28193
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.659 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.667 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.713 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.748 1.850
  nonbonded model="   0" pdb=" O   GLY A  73 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.827 1.850
  ... (remaining 28188 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   5.84 %
                favored =  86.86 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.53
  MolProbity score      =   1.94

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.212, 58.939, 68.918, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.587, 84.904, 45.912, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  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.


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  2.467)
  Mean delta:    0.012 (Z=  0.622)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.474 (Z=  3.998)
  Mean delta:    1.577 (Z=  0.854)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   156.91    23.09  5.00e+00  2.13e+01   4.6*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   158.72    21.28  5.00e+00  1.81e+01   4.3*sigma

  Min. delta:    0.019
  Max. delta:   89.195
  Mean delta:   13.138

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.239
  Mean delta:    0.079

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.075
  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   2242  Z= 0.443
    Angle     :  1.529   6.474   4079  Z= 0.657
    Chirality :  0.079   0.239    176
    Planarity :  0.009   0.056    327
    Dihedral  : 11.714  89.195    769
    Min Nonbonded Distance : 1.481
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.03 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.12 (0.67), residues: 137
    helix:  0.05 (0.48), residues: 88
    sheet:  None (None), residues: 0
    loop : -0.03 (0.95), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.070   0.010   TYR A  50 
   ARG   0.061   0.014   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.058   0.012   TYR A  50 
   ARG   0.006   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 2
        1.22 -     1.42: 462
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.297  0.032 1.40e-02 5.10e+03 5.32e+00
  bond model="   0" pdb=" C   HIS A 136 "
       model="   0" pdb=" N   HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 1.97e+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 1.75e+00
  bond model="   0" pdb=" C   ASP A 116 "
       model="   0" pdb=" N   PRO A 117 "
    ideal  model  delta    sigma   weight residual
    1.341  1.323  0.018 1.60e-02 3.91e+03 1.29e+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 1.09e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.12 -   106.28: 47
      106.28 -   112.45: 2702
      112.45 -   118.61: 443
      118.61 -   124.77: 844
      124.77 -   130.94: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.93   -4.93 3.00e+00 1.11e-01 2.70e+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  113.53   -4.53 3.00e+00 1.11e-01 2.28e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.52   -4.52 3.00e+00 1.11e-01 2.27e+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  104.48    4.52 3.00e+00 1.11e-01 2.27e+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  105.51    4.49 3.00e+00 1.11e-01 2.24e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.19: 983
       16.19 -    32.38: 25
       32.38 -    48.56: 13
       48.56 -    64.75: 5
       64.75 -    80.94: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -80.94   80.94     1      3.00e+01 1.11e-03 8.99e+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  -80.18   50.18     1      2.00e+01 2.50e-03 8.63e+00
  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   70.55  -70.55     1      3.00e+01 1.11e-03 7.12e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 124
       0.033 -    0.065: 38
       0.065 -    0.097: 7
       0.097 -    0.129: 6
       0.129 -    0.161: 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    2.59   -0.16 2.00e-01 2.50e+01 6.49e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.55e-01
  chirality model="   0" pdb=" CA  VAL A  57 "
            model="   0" pdb=" N   VAL A  57 "
            model="   0" pdb=" C   VAL A  57 "
            model="   0" pdb=" CB  VAL A  57 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.11 2.00e-01 2.50e+01 3.27e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.014 5.00e-02 4.00e+02   2.14e-02 7.31e-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 "    0.007 2.00e-02 2.50e+03   4.33e-03 5.63e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.000 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 "   -0.010 2.00e-02 2.50e+03   4.03e-03 4.87e-01
        model="   0" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.52 -     2.14: 98
        2.14 -     2.75: 4228
        2.75 -     3.37: 6081
        3.37 -     3.98: 7659
        3.98 -     4.60: 11604
  Nonbonded interactions: 29670
  Sorted by model distance:
  nonbonded model="   0" pdb="HH12 ARG A 127 "
            model="   0" pdb=" OE1 GLU A 133 "
     model   vdw
     1.521 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.588 1.850
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD11 ILE A  78 "
     model   vdw
     1.599 2.440
  nonbonded model="   0" pdb=" OG1 THR A  83 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.607 1.850
  nonbonded model="   0" pdb=" OE1 GLU A   8 "
            model="   0" pdb=" HE  ARG A  58 "
     model   vdw
     1.674 1.850
  ... (remaining 29665 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: 84
        1.23 -     1.43: 388
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A  58 "
       model="   0" pdb=" NH2 ARG A  58 "
    ideal  model  delta    sigma   weight residual
    1.330  1.290  0.040 1.30e-02 5.92e+03 9.59e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.20e+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 6.25e+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 6.19e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.85e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.21 -   106.12: 95
      106.12 -   112.03: 2549
      112.03 -   117.93: 461
      117.93 -   123.84: 865
      123.84 -   129.74: 109
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.10    5.10 1.30e+00 5.92e-01 1.54e+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  116.26   -3.66 1.00e+00 1.00e+00 1.34e+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  126.47    4.73 1.30e+00 5.92e-01 1.32e+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  126.61    4.59 1.30e+00 5.92e-01 1.24e+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  126.77    4.43 1.30e+00 5.92e-01 1.16e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 971
       17.88 -    35.76: 39
       35.76 -    53.63: 11
       53.63 -    71.51: 5
       71.51 -    89.39: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.90   27.10     0      5.00e+00 4.00e-02 2.94e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.02   24.98     0      5.00e+00 4.00e-02 2.50e+01
  dihedral model="   0" pdb=" CA  ILE A  51 "
           model="   0" pdb=" C   ILE A  51 "
           model="   0" pdb=" N   PRO A  52 "
           model="   0" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.13   23.87     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 71
       0.035 -    0.070: 49
       0.070 -    0.105: 28
       0.105 -    0.140: 22
       0.140 -    0.175: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.69e-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 6.21e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.07e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.075 2.00e-02 2.50e+03   2.98e-02 2.66e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.007 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 "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.045 2.00e-02 2.50e+03   2.18e-02 1.42e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.007 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 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 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 "   -0.047 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 "    0.022 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 "    0.012 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   2.01e-02 1.21e+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 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 36
        2.03 -     2.68: 3129
        2.68 -     3.32: 6393
        3.32 -     3.96: 7522
        3.96 -     4.60: 11435
  Nonbonded interactions: 28515
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  88 "
            model="   0" pdb=" HZ2 LYS A 101 "
     model   vdw
     1.393 1.850
  nonbonded model="   0" pdb=" OE2 GLU A   8 "
            model="   0" pdb="HH21 ARG A  58 "
     model   vdw
     1.525 1.850
  nonbonded model="   0" pdb=" OH  TYR A  50 "
            model="   0" pdb="HH22 ARG A 129 "
     model   vdw
     1.683 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.744 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  32 "
            model="   0" pdb="HD21 ASN A  72 "
     model   vdw
     1.783 1.850
  ... (remaining 28510 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   7.66
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.53
  MolProbity score      =   1.75

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

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

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

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

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

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

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

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

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

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

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

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


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

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.869)
  Mean delta:    0.012 (Z=  0.642)

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

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

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.284 (Z=  4.276)
  Mean delta:    1.555 (Z=  0.856)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.034
  Max. delta:   83.676
  Mean delta:   12.603

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.194
  Mean delta:    0.074

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.069
  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   2242  Z= 0.457
    Angle     :  1.510   6.284   4079  Z= 0.655
    Chirality :  0.074   0.194    176
    Planarity :  0.008   0.052    327
    Dihedral  : 11.101  83.676    769
    Min Nonbonded Distance : 1.687
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  0.81 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.36 (0.70), residues: 137
    helix:  0.04 (0.48), residues: 92
    sheet: -0.22 (1.87), residues: 10
    loop :  1.57 (1.24), residues: 35
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 136 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.054   0.009   TYR A  50 
   ARG   0.056   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 136 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.045   0.010   TYR A  50 
   ARG   0.006   0.002   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.76, per 1000 atoms: 0.34
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.17, 60.177, 52.191, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   3.16
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.51
  MolProbity score      =   1.66

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

End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  1.888)
  Mean delta:    0.005 (Z=  0.301)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    5.076 (Z=  1.813)
  Mean delta:    0.777 (Z=  0.365)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.008
  Max. delta:   84.374
  Mean delta:   11.296

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.177
  Mean delta:    0.045

                       ----------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      :  0.004   0.038   2242  Z= 0.214
    Angle     :  1.099   5.334   4079  Z= 0.399
    Chirality :  0.045   0.177    176
    Planarity :  0.003   0.021    327
    Dihedral  : 10.986  84.374    769
    Min Nonbonded Distance : 1.708
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.02 (0.69), residues: 137
    helix: -0.07 (0.59), residues: 71
    sheet:  None (None), residues: 0
    loop :  0.33 (0.76), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.008   0.002   PHE A  15 
   TYR   0.012   0.003   TYR A  50 
   ARG   0.008   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.006   0.002   PHE A  15 
   TYR   0.009   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 ===================================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

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

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

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

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

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0037
  RMS(angles)           =   1.10
  MolProbity score      =   1.36

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

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


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

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

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


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

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

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

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

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


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


  Symmetric amino acids flipped
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.1, 64.775, 34.574, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.93 seconds

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

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

End of input processing

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

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  2.832)
  Mean delta:    0.012 (Z=  0.628)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.375 (Z=  3.729)
  Mean delta:    1.617 (Z=  0.883)

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

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   152.95    27.05  5.00e+00  2.93e+01   5.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   156.84    23.16  5.00e+00  2.15e+01   4.6*sigma

  Min. delta:    0.017
  Max. delta:   88.800
  Mean delta:   12.952

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.193
  Mean delta:    0.080

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.069
  Mean delta:    0.012

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.042   2242  Z= 0.447
    Angle     :  1.557   6.375   4079  Z= 0.674
    Chirality :  0.080   0.193    176
    Planarity :  0.008   0.051    327
    Dihedral  : 11.648  88.800    769
    Min Nonbonded Distance : 1.303
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  4.38 %
      Favored  : 93.43 %
    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: -0.46 (0.67), residues: 137
    helix: -0.33 (0.48), residues: 84
    sheet:  None (None), residues: 0
    loop :  0.04 (0.94), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.030   0.007   PHE A  15 
   TYR   0.066   0.011   TYR A 111 
   ARG   0.055   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.020   0.007   PHE A  15 
   TYR   0.055   0.013   TYR A  50 
   ARG   0.007   0.001   ARG A 127 

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

  No backwards Asn/Gln/His sidechains found.

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 118
        1.23 -     1.43: 354
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.56e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.27e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.77e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.67e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.60e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.89 -   106.73: 165
      106.73 -   112.56: 2548
      112.56 -   118.40: 434
      118.40 -   124.24: 839
      124.24 -   130.08: 93
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   ASP A  95 "
        model="   0" pdb=" N   GLY A  96 "
        model="   0" pdb=" CA  GLY A  96 "
      ideal   model   delta    sigma   weight residual
     121.70  130.08   -8.38 1.80e+00 3.09e-01 2.16e+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  118.63    3.97 1.00e+00 1.00e+00 1.57e+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  119.00    3.60 1.00e+00 1.00e+00 1.30e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.12   -3.52 1.00e+00 1.00e+00 1.24e+01
  angle model="   0" pdb=" CB  HIS A 138 "
        model="   0" pdb=" CG  HIS A 138 "
        model="   0" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  126.70    4.50 1.30e+00 5.92e-01 1.20e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 963
       17.27 -    34.55: 52
       34.55 -    51.82: 14
       51.82 -    69.09: 2
       69.09 -    86.36: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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  154.57   25.43     0      5.00e+00 4.00e-02 2.59e+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  157.80   22.20     0      5.00e+00 4.00e-02 1.97e+01
  dihedral model="   0" pdb=" CA  GLU A 123 "
           model="   0" pdb=" C   GLU A 123 "
           model="   0" pdb=" N   ALA A 124 "
           model="   0" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.66  -20.34     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 68
       0.038 -    0.075: 47
       0.075 -    0.112: 27
       0.112 -    0.149: 27
       0.149 -    0.187: 7
  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 8.72e-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    0.19 2.00e-01 2.50e+01 8.57e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.18 2.00e-01 2.50e+01 8.20e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.114 2.00e-02 2.50e+03   5.29e-02 8.39e+01
        model="   0" pdb=" CG  TYR A  81 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.110 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.035 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.086 2.00e-02 2.50e+03   3.81e-02 4.35e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.018 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 "    0.013 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 "   -0.078 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.050 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 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 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 "   -0.031 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 "    0.017 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
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 37
        2.03 -     2.67: 3106
        2.67 -     3.32: 6255
        3.32 -     3.96: 7220
        3.96 -     4.60: 11065
  Nonbonded interactions: 27683
  Sorted by model distance:
  nonbonded model="   0" pdb=" OH  TYR A  81 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.390 1.850
  nonbonded model="   0" pdb=" OH  TYR A  81 "
            model="   0" pdb=" HA  LEU A  93 "
     model   vdw
     1.402 2.620
  nonbonded model="   0" pdb=" HE1 TYR A  81 "
            model="   0" pdb=" O   THR A  92 "
     model   vdw
     1.524 2.450
  nonbonded model="   0" pdb=" HH  TYR A  81 "
            model="   0" pdb=" H   GLY A  94 "
     model   vdw
     1.707 2.100
  nonbonded model="   0" pdb=" HZ2 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.713 1.850
  ... (remaining 27678 not shown)

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

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


End of input processing

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

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

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


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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.666)
  Mean delta:    0.012 (Z=  0.626)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.397 (Z=  3.929)
  Mean delta:    1.578 (Z=  0.859)

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.007
  Max. delta:   86.612
  Mean delta:   12.565

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

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.202
  Mean delta:    0.075

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

  All restrained atoms within 4.0 sigma of ideal values.

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

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


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

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

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

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

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

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

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


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.446
    Angle     :  1.530   7.397   4079  Z= 0.659
    Chirality :  0.075   0.202    176
    Planarity :  0.007   0.036    327
    Dihedral  : 11.143  86.612    769
    Min Nonbonded Distance : 1.555
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  3.23 %
      Favored  : 92.74 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.65 (0.72), residues: 137
    helix:  0.51 (0.52), residues: 85
    sheet:  None (None), residues: 0
    loop :  0.59 (1.00), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.062   0.009   TYR A 111 
   ARG   0.035   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.010   0.003   PHE A  67 
   TYR   0.052   0.010   TYR A 111 
   ARG   0.005   0.001   ARG A  21 

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

  No backwards Asn/Gln/His sidechains found.

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

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.189, 53.667, 67.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (37.471, 81.445, 48.362, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   2.19 %
                favored =  93.43 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.56
  MolProbity score      =   2.00

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 0.95, per 1000 atoms: 0.43
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.091, 73.678, 47.394, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.53
  MolProbity score      =   1.85

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.205, 58.535, 74.088, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.31, per 1000 atoms: 0.59
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.005, 67.096, 59.953, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

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


  Symmetric amino acids flipped
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

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

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

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

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

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

  Time building geometry restraints manager: 1.17 seconds

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


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

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

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

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

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

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 104
        1.23 -     1.43: 368
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.13e+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 5.97e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.77e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.50e+00
  bond model="   0" pdb=" CB  THR A  82 "
       model="   0" pdb=" OG1 THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.433  1.396  0.037 1.60e-02 3.91e+03 5.29e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.27 -   106.02: 91
      106.02 -   111.77: 2481
      111.77 -   117.52: 494
      117.52 -   123.27: 818
      123.27 -   129.03: 195
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.50    4.10 1.00e+00 1.00e+00 1.68e+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  119.00    3.60 1.00e+00 1.00e+00 1.30e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.87    4.33 1.30e+00 5.92e-01 1.11e+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  129.03   -4.63 1.40e+00 5.10e-01 1.09e+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  127.05    4.15 1.30e+00 5.92e-01 1.02e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 968
       17.89 -    35.77: 45
       35.77 -    53.66: 16
       53.66 -    71.55: 3
       71.55 -    89.43: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.51   23.49     0      5.00e+00 4.00e-02 2.21e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.08   18.92     0      5.00e+00 4.00e-02 1.43e+01
  dihedral model="   0" pdb=" CA  GLY A  96 "
           model="   0" pdb=" C   GLY A  96 "
           model="   0" pdb=" N   SER A  97 "
           model="   0" pdb=" CA  SER A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.90   17.10     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 69
       0.040 -    0.080: 45
       0.080 -    0.120: 40
       0.120 -    0.160: 19
       0.160 -    0.200: 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 1.00e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.21e-01
  chirality model="   0" pdb=" CA  SER A  97 "
            model="   0" pdb=" N   SER A  97 "
            model="   0" pdb=" C   SER A  97 "
            model="   0" pdb=" CB  SER A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.42e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "    0.123 2.00e-02 2.50e+03   4.90e-02 7.21e+01
        model="   0" pdb=" CG  PHE A  15 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "    0.064 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.072 2.00e-02 2.50e+03   3.12e-02 2.92e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.062 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.019 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   1.95e-02 1.14e+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 "   -0.012 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 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 122
        2.15 -     2.76: 4071
        2.76 -     3.37: 6261
        3.37 -     3.99: 7636
        3.99 -     4.60: 11488
  Nonbonded interactions: 29578
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   THR A  82 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     1.536 2.620
  nonbonded model="   0" pdb="HD21 LEU A  93 "
            model="   0" pdb=" HB2 LEU A  99 "
     model   vdw
     1.579 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.706 1.850
  nonbonded model="   0" pdb="HG23 THR A  83 "
            model="   0" pdb=" HA  THR A  92 "
     model   vdw
     1.709 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.741 1.850
  ... (remaining 29573 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.587, 84.904, 45.912, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (78.913, 46.038, 64.309, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
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: 1.21, per 1000 atoms: 0.55
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.604, 70.183, 55.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.68
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.80 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 6
        1.23 -     1.42: 457
        1.42 -     1.61: 669
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   GLU A 120 "
       model="   0" pdb=" N   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.18e+00
  bond model="   0" pdb=" C   GLU A 123 "
       model="   0" pdb=" N   ALA A 124 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.94e+00
  bond model="   0" pdb=" C   GLU A 133 "
       model="   0" pdb=" N   HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.329  1.348 -0.019 1.40e-02 5.10e+03 1.91e+00
  bond model="   0" pdb=" C   ARG A 127 "
       model="   0" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.72e+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 1.63e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.28 -   106.44: 47
      106.44 -   112.60: 2719
      112.60 -   118.75: 440
      118.75 -   124.91: 831
      124.91 -   131.07: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.00   -5.00 3.00e+00 1.11e-01 2.78e+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  113.77   -4.77 3.00e+00 1.11e-01 2.53e+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  104.35    4.65 3.00e+00 1.11e-01 2.40e+00
  angle model="   0" pdb=" CB  PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.49   -4.49 3.00e+00 1.11e-01 2.24e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.48   -4.48 3.00e+00 1.11e-01 2.23e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.25: 985
       16.25 -    32.51: 29
       32.51 -    48.76: 14
       48.76 -    65.02: 3
       65.02 -    81.27: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A 133 "
           model="   0" pdb=" CB  GLU A 133 "
           model="   0" pdb=" CG  GLU A 133 "
           model="   0" pdb=" CD  GLU A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -108.54   48.54     3      1.50e+01 4.44e-03 8.65e+00
  dihedral model="   0" pdb=" CA  ASP A 116 "
           model="   0" pdb=" CB  ASP A 116 "
           model="   0" pdb=" CG  ASP A 116 "
           model="   0" pdb=" OD1 ASP A 116 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -75.85   45.85     1      2.00e+01 2.50e-03 7.28e+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
     -30.00  -74.64   44.64     1      2.00e+01 2.50e-03 6.92e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 132
       0.028 -    0.057: 25
       0.057 -    0.085: 6
       0.085 -    0.113: 11
       0.113 -    0.142: 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   -0.14 2.00e-01 2.50e+01 5.02e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.38e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.12e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 "    0.008 2.00e-02 2.50e+03   5.46e-03 5.97e-01
        model="   0" pdb=" CG  HIS A 139 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.009 2.00e-02 2.50e+03   4.26e-03 5.45e-01
        model="   0" pdb=" CG  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 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 "   -0.002 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 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 138 "   -0.007 2.00e-02 2.50e+03   5.03e-03 5.06e-01
        model="   0" pdb=" CG  HIS A 138 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 138 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 138 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 138 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 138 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 138 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 138 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.26: 280
        2.26 -     2.85: 5231
        2.85 -     3.43: 5531
        3.43 -     4.02: 7528
        4.02 -     4.60: 11332
  Nonbonded interactions: 29902
  Sorted by model distance:
  nonbonded model="   0" pdb=" H   LEU A  93 "
            model="   0" pdb=" O   SER A  97 "
     model   vdw
     1.679 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.715 2.270
  nonbonded model="   0" pdb=" O   GLU A 133 "
            model="   0" pdb=" H   HIS A 135 "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.777 1.850
  nonbonded model="   0" pdb=" O   GLU A  16 "
            model="   0" pdb=" HG1 THR A  20 "
     model   vdw
     1.786 1.850
  ... (remaining 29897 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.97, 47.568, 50.518, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

  Time building chain proxies: 0.93, per 1000 atoms: 0.42
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (97.797, 52.024, 48.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.07, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.98, 59.858, 46.737, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (39.573, 54.984, 70.573, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  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.


  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.81 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 5
        1.23 -     1.42: 458
        1.42 -     1.61: 669
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.258 -0.027 2.00e-02 2.50e+03 1.81e+00
  bond model="   0" pdb=" C   ARG A 127 "
       model="   0" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.66e+00
  bond model="   0" pdb=" C   ASP A  74 "
       model="   0" pdb=" N   GLU A  75 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.42e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.41e+00
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.32e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.70 -   106.73: 59
      106.73 -   112.76: 2704
      112.76 -   118.79: 442
      118.79 -   124.83: 832
      124.83 -   130.86: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  123.07   -5.07 3.00e+00 1.11e-01 2.86e+00
  angle model="   0" pdb=" N   ILE A  78 "
        model="   0" pdb=" CA  ILE A  78 "
        model="   0" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.00  104.96    5.04 3.00e+00 1.11e-01 2.82e+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  104.04    4.96 3.00e+00 1.11e-01 2.73e+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  113.84   -4.84 3.00e+00 1.11e-01 2.61e+00
  angle model="   0" pdb=" N   ILE A  77 "
        model="   0" pdb=" CA  ILE A  77 "
        model="   0" pdb=" HA  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     110.00  105.24    4.76 3.00e+00 1.11e-01 2.51e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 985
       17.27 -    34.55: 22
       34.55 -    51.82: 13
       51.82 -    69.10: 6
       69.10 -    86.37: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" CB  ASP A 118 "
           model="   0" pdb=" CG  ASP A 118 "
           model="   0" pdb=" OD1 ASP A 118 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.67   56.67     1      2.00e+01 2.50e-03 1.08e+01
  dihedral model="   0" pdb=" CA  ASP A  95 "
           model="   0" pdb=" CB  ASP A  95 "
           model="   0" pdb=" CG  ASP A  95 "
           model="   0" pdb=" OD1 ASP A  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.24   56.24     1      2.00e+01 2.50e-03 1.07e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.37  -86.37     1      3.00e+01 1.11e-03 9.99e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 101
       0.029 -    0.057: 59
       0.057 -    0.085: 4
       0.085 -    0.114: 8
       0.114 -    0.142: 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    2.58   -0.14 2.00e-01 2.50e+01 5.06e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.014 2.00e-02 2.50e+03   5.48e-03 9.02e-01
        model="   0" pdb=" CG  TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.000 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.013 2.00e-02 2.50e+03   5.43e-03 8.84e-01
        model="   0" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.011 2.00e-02 2.50e+03   4.43e-03 5.89e-01
        model="   0" pdb=" CG  TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.25 -     1.92: 21
        1.92 -     2.59: 2403
        2.59 -     3.26: 6839
        3.26 -     3.93: 8198
        3.93 -     4.60: 12729
  Nonbonded interactions: 30190
  Sorted by model distance:
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" O   TYR A  89 "
     model   vdw
     1.252 2.620
  nonbonded model="   0" pdb=" HD2 TYR A  89 "
            model="   0" pdb="HD21 LEU A  99 "
     model   vdw
     1.494 2.270
  nonbonded model="   0" pdb=" OE2 GLU A  75 "
            model="   0" pdb=" HZ3 LYS A  79 "
     model   vdw
     1.500 1.850
  nonbonded model="   0" pdb=" HE1 PHE A  67 "
            model="   0" pdb="HD13 LEU A  99 "
     model   vdw
     1.569 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  36 "
            model="   0" pdb=" HE2 LYS A  40 "
     model   vdw
     1.638 2.620
  ... (remaining 30185 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.96 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.94
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.02 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 103
        1.23 -     1.43: 369
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.08e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.64e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.14e+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 6.73e+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 6.22e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.80 -   105.66: 63
      105.66 -   111.52: 2449
      111.52 -   117.38: 549
      117.38 -   123.24: 823
      123.24 -   129.10: 195
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  HIS A 138 "
        model="   0" pdb=" CG  HIS A 138 "
        model="   0" pdb=" CD2 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     131.20  126.33    4.87 1.30e+00 5.92e-01 1.41e+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  126.51    4.69 1.30e+00 5.92e-01 1.30e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.52    4.68 1.30e+00 5.92e-01 1.30e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.04    3.56 1.00e+00 1.00e+00 1.27e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.70    4.50 1.30e+00 5.92e-01 1.20e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 975
       17.85 -    35.69: 41
       35.69 -    53.54: 11
       53.54 -    71.39: 4
       71.39 -    89.24: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.70   28.30     0      5.00e+00 4.00e-02 3.20e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.46   26.54     0      5.00e+00 4.00e-02 2.82e+01
  dihedral model="   0" pdb=" CA  LEU A  93 "
           model="   0" pdb=" C   LEU A  93 "
           model="   0" pdb=" N   GLY A  94 "
           model="   0" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.62   18.38     0      5.00e+00 4.00e-02 1.35e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 80
       0.042 -    0.084: 50
       0.084 -    0.126: 32
       0.126 -    0.168: 12
       0.168 -    0.210: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LEU A 119 "
            model="   0" pdb=" N   LEU A 119 "
            model="   0" pdb=" C   LEU A 119 "
            model="   0" pdb=" CB  LEU A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.37e-01
  chirality model="   0" pdb=" CG  LEU A 132 "
            model="   0" pdb=" CB  LEU A 132 "
            model="   0" pdb=" CD1 LEU A 132 "
            model="   0" pdb=" CD2 LEU A 132 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.60e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "   -0.098 2.00e-02 2.50e+03   3.93e-02 4.63e+01
        model="   0" pdb=" CG  PHE A  15 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "   -0.052 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.048 2.00e-02 2.50e+03   2.17e-02 1.41e+01
        model="   0" pdb=" CG  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.045 2.00e-02 2.50e+03   1.86e-02 1.04e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.008 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 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.005 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 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 50
        2.00 -     2.65: 2907
        2.65 -     3.30: 6701
        3.30 -     3.95: 7876
        3.95 -     4.60: 12080
  Nonbonded interactions: 29614
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  86 "
            model="   0" pdb=" HB2 TYR A  89 "
     model   vdw
     1.352 2.440
  nonbonded model="   0" pdb=" HB3 LEU A  70 "
            model="   0" pdb="HD11 ILE A  78 "
     model   vdw
     1.393 2.440
  nonbonded model="   0" pdb=" HH  TYR A  12 "
            model="   0" pdb=" HE1 TYR A  89 "
     model   vdw
     1.446 2.100
  nonbonded model="   0" pdb=" HE1 PHE A  15 "
            model="   0" pdb=" HB3 TYR A  81 "
     model   vdw
     1.571 2.270
  nonbonded model="   0" pdb="HD12 ILE A  78 "
            model="   0" pdb="HD22 LEU A  99 "
     model   vdw
     1.610 2.440
  ... (remaining 29609 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.385, 51.843, 44.039, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 76
        1.23 -     1.43: 396
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 8.74e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.33e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.72e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.60e+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 5.53e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.30 -   106.03: 106
      106.03 -   111.76: 2466
      111.76 -   117.49: 497
      117.49 -   123.23: 813
      123.23 -   128.96: 197
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.41    4.19 1.00e+00 1.00e+00 1.76e+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
  angle model="   0" pdb=" N   LEU A  93 "
        model="   0" pdb=" CA  LEU A  93 "
        model="   0" pdb=" C   LEU A  93 "
      ideal   model   delta    sigma   weight residual
     111.00  101.52    9.48 2.80e+00 1.28e-01 1.15e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.95   -3.35 1.00e+00 1.00e+00 1.12e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.26    3.34 1.00e+00 1.00e+00 1.12e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.66: 952
       16.66 -    33.32: 62
       33.32 -    49.99: 11
       49.99 -    66.65: 6
       66.65 -    83.31: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.99   38.01     0      5.00e+00 4.00e-02 5.78e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.39   35.61     0      5.00e+00 4.00e-02 5.07e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.11   34.89     0      5.00e+00 4.00e-02 4.87e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 74
       0.049 -    0.098: 65
       0.098 -    0.147: 30
       0.147 -    0.196: 4
       0.196 -    0.244: 3
  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    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.064 2.00e-02 2.50e+03   2.77e-02 2.31e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 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   2.10e-02 1.33e+01
        model="   0" pdb=" CG  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 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 "    0.013 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 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.047 2.00e-02 2.50e+03   1.83e-02 1.00e+01
        model="   0" pdb=" CG  TYR A  12 "    0.013 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 "    0.004 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 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 398
        2.32 -     2.89: 5198
        2.89 -     3.46: 5270
        3.46 -     4.03: 6725
        4.03 -     4.60: 10091
  Nonbonded interactions: 27682
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.753 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.763 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.765 1.850
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" HE2 TYR A  81 "
     model   vdw
     1.797 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.834 1.850
  ... (remaining 27677 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  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 91
        1.23 -     1.43: 381
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.63e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.385 -0.031 1.10e-02 8.26e+03 8.10e+00
  bond model="   0" pdb=" CB  THR A  82 "
       model="   0" pdb=" OG1 THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.433  1.388  0.045 1.60e-02 3.91e+03 7.92e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.45e+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 6.87e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   106.17: 93
      106.17 -   111.79: 2503
      111.79 -   117.42: 468
      117.42 -   123.05: 792
      123.05 -   128.68: 223
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.51    4.09 1.00e+00 1.00e+00 1.67e+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  126.17    5.03 1.30e+00 5.92e-01 1.50e+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  126.24    4.96 1.30e+00 5.92e-01 1.45e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.09    3.51 1.00e+00 1.00e+00 1.23e+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  126.78    4.42 1.30e+00 5.92e-01 1.16e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 977
       17.97 -    35.95: 34
       35.95 -    53.92: 17
       53.92 -    71.90: 3
       71.90 -    89.87: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.39   18.61     0      5.00e+00 4.00e-02 1.39e+01
  dihedral model="   0" pdb=" N   ARG A 129 "
           model="   0" pdb=" CA  ARG A 129 "
           model="   0" pdb=" CB  ARG A 129 "
           model="   0" pdb=" CG  ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.15  -57.85     3      1.50e+01 4.44e-03 9.45e+00
  dihedral model="   0" pdb=" CA  LEU A  99 "
           model="   0" pdb=" CB  LEU A  99 "
           model="   0" pdb=" CG  LEU A  99 "
           model="   0" pdb=" CD1 LEU A  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  126.00   54.00     3      1.50e+01 4.44e-03 9.25e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 88
       0.050 -    0.101: 53
       0.101 -    0.151: 28
       0.151 -    0.201: 5
       0.201 -    0.251: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.38e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.068 2.00e-02 2.50e+03   2.92e-02 2.56e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.016 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   1.86e-02 1.04e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.046 2.00e-02 2.50e+03   1.79e-02 9.58e+00
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.012 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 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.028 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 "    0.015 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
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 86
        2.11 -     2.73: 3754
        2.73 -     3.35: 6157
        3.35 -     3.98: 7656
        3.98 -     4.60: 11286
  Nonbonded interactions: 28939
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ3 LYS A 113 "
            model="   0" pdb=" OE1 GLU A 120 "
     model   vdw
     1.487 1.850
  nonbonded model="   0" pdb="HD22 LEU A  93 "
            model="   0" pdb="HD12 LEU A  99 "
     model   vdw
     1.515 2.440
  nonbonded model="   0" pdb=" OG  SER A  76 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.540 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.544 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.547 1.850
  ... (remaining 28934 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: 106
        1.23 -     1.43: 366
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.44e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.12e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.90e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.65e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.63e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.90 -   105.70: 66
      105.70 -   111.51: 2432
      111.51 -   117.31: 560
      117.31 -   123.11: 803
      123.11 -   128.91: 218
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.32    4.28 1.00e+00 1.00e+00 1.83e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.47    4.73 1.30e+00 5.92e-01 1.33e+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=" 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=" 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  126.91    4.29 1.30e+00 5.92e-01 1.09e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 958
       17.79 -    35.58: 55
       35.58 -    53.38: 15
       53.38 -    71.17: 3
       71.17 -    88.96: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  94 "
           model="   0" pdb=" C   GLY A  94 "
           model="   0" pdb=" N   ASP A  95 "
           model="   0" pdb=" CA  ASP A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.70  -26.30     0      5.00e+00 4.00e-02 2.77e+01
  dihedral model="   0" pdb=" CA  ASP A  74 "
           model="   0" pdb=" C   ASP A  74 "
           model="   0" pdb=" N   GLU A  75 "
           model="   0" pdb=" CA  GLU A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.07   22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.02   19.98     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 75
       0.047 -    0.094: 54
       0.094 -    0.140: 37
       0.140 -    0.187: 6
       0.187 -    0.234: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A  74 "
            model="   0" pdb=" N   ASP A  74 "
            model="   0" pdb=" C   ASP A  74 "
            model="   0" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.165 2.00e-02 2.50e+03   7.44e-02 1.66e+02
        model="   0" pdb=" CG  TYR A  89 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.153 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.043 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.062 2.00e-02 2.50e+03   2.69e-02 2.17e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.016 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   1.89e-02 1.07e+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 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 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 "    0.031 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 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.03: 48
        2.03 -     2.67: 314Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

7
        2.67 -     3.31: 6510
        3.31 -     3.96: 7833
        3.96 -     4.60: 11751
  Nonbonded interactions: 29289
  Sorted by model distance:
  nonbonded model="   0" pdb=" CE2 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.385 2.970
  nonbonded model="   0" pdb=" O   GLY A  80 "
            model="   0" pdb=" HB3 LEU A  93 "
     model   vdw
     1.444 2.620
  nonbonded model="   0" pdb=" HE2 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.569 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb="HG13 ILE A  77 "
     model   vdw
     1.625 2.620
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.651 1.850
  ... (remaining 29284 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 119
        1.23 -     1.43: 353
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   MET A   1 "
       model="   0" pdb=" N   LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.034 1.40e-02 5.10e+03 5.91e+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 5.83e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.77e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.75e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.66e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.59 -   106.24: 114
      106.24 -   111.89: 2479
      111.89 -   117.53: 480
      117.53 -   123.18: 806
      123.18 -   128.83: 200
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.61    3.99 1.00e+00 1.00e+00 1.59e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.42   -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  126.29    4.91 1.30e+00 5.92e-01 1.43e+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  119.16    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  126.94    4.26 1.30e+00 5.92e-01 1.07e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 974
       17.99 -    35.98: 41
       35.98 -    53.97: 12
       53.97 -    71.96: 2
       71.96 -    89.94: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   LYS A  85 "
           model="   0" pdb=" CA  LYS A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.51   25.49     0      5.00e+00 4.00e-02 2.60e+01
  dihedral model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" C   HIS A 137 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.50   23.50     0      5.00e+00 4.00e-02 2.21e+01
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.11  -22.89     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.039: 67
       0.039 -    0.076: 46
       0.076 -    0.113: 34
       0.113 -    0.150: 26
     Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 58
        1.23 -     1.42: 414
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.68e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.11e+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 6.44e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.74e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.46e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.26 -   106.02: 85
      106.02 -   111.77: 2504
      111.77 -   117.53: 482
      117.53 -   123.28: 818
      123.28 -   129.04: 190
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.57    4.03 1.00e+00 1.00e+00 1.62e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.29   -3.69 1.00e+00 1.00e+00 1.36e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.48    4.72 1.30e+00 5.92e-01 1.32e+01
  angle model="   0" pdb=" 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  126.56    4.64 1.30e+00 5.92e-01 1.27e+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  116.11   -3.51 1.00e+00 1.00e+00 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 961
       16.29 -    32.58: 45
       32.58 -    48.88: 15
       48.88 -    65.17: 9
       65.17 -    81.46: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.73   23.27     0      5.00e+00 4.00e-02 2.17e+01
  dihedral model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
           model="   0" pdb=" CB  HIS A 139 "
           model="   0" pdb=" CG  HIS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.83  -58.17     3      1.50e+01 4.44e-03 9.46e+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  164.63   15.37     0      5.00e+00 4.00e-02 9.45e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 71
       0.040 -    0.080: 45
       0.080 -    0.120: 38
       0.120 -    0.160: 18
         0.150 -    0.188: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.79e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.20e-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   -2.75    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.061 2.00e-02 2.50e+03   2.64e-02 2.08e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.067 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.023 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.056 2.00e-02 2.50e+03   2.22e-02 1.48e+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 "    0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.020 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 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 27
        2.00 -     2.65: 2808
        2.65 -     3.30: 6531
        3.30 -     3.95: 7436
        3.95 -     4.60: 11434
  Nonbonded interactions: 28236
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  86 "
            model="   0" pdb=" H   GLY A  87 "
     model   vdw
     1.350 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.654 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.715 1.850
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" HD1 TYR A  91 "
     model   vdw
     1.727 2.270
  nonbonded model="   0" pdb=" HZ2 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.738 1.850
  ... (remaining 28231 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  0.160 -    0.200: 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    2.31    0.20 2.00e-01 2.50e+01 9.99e-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 8.28e-01
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.44e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.149 2.00e-02 2.50e+03   6.38e-02 1.22e+02
        model="   0" pdb=" CG  TYR A  81 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.123 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.033 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.022 2.00e-02 2.50e+03   4.54e-02 2.06e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.079 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.058 2.00e-02 2.50e+03   2.62e-02 2.06e+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 "   -0.012 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 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 112
        2.15 -     2.76: 4093
        2.76 -     3.37: 6248
        3.37 -     3.99: 7566
        3.99 -     4.60: 11382
  Nonbonded interactions: 29401
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.537 1.850
  nonbonded model="   0" pdb=" HD1 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.555 2.270
  nonbonded model="   0" pdb="HG23 ILE A  78 "
            model="   0" pdb="HD22 LEU A  93 "
     model   vdw
     1.606 2.440
  nonbonded model="   0" pdb=" HB2 TYR A  81 "
            model="   0" pdb="HD13 LEU A  93 "
     model   vdw
     1.687 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.705 1.850
  ... (remaining 29396 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  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  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.

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.461, 62.592, 57.417, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.130)
  Mean delta:    0.012 (Z=  0.639)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.58     4.02  1.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    6.231 (Z=  4.017)
  Mean delta:    1.632 (Z=  0.893)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   156.77    23.23  5.00e+00  2.16e+01   4.6*sigma

  Min. delta:    0.001
  Max. delta:   81.260
  Mean delta:   11.926

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.208
  Mean delta:    0.078

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.081       0.149      131.90   7.5*sigma

  Min. delta:    0.000
  Max. delta:    0.081
  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      :  0.009   0.040   2242  Z= 0.455
    Angle     :  1.562   6.231   4079  Z= 0.679
    Chirality :  0.078   0.208    176
    Planarity :  0.009   0.076    327
    Dihedral  : 11.033  81.260    769
    Min Nonbonded Distance : 1.596
  
  Molprobity Statistics.
    All-atom Clashscore : 9.02
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  4.03 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.18 (0.69), residues: 137
    helix:  0.13 (0.51), residues: 81
    sheet: -3.12 (1.11), residues: 10
    loop :  1.35 (1.02), residues: 46
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.021   0.004   PHE A  67 
   TYR   0.182   0.021   TYR A  89 
   ARG   0.048   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.149   0.025   TYR A  89 
   ARG   0.005   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 1.08, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.079, 56.762, 55.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 68
        1.23 -     1.43: 404
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.59e+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 6.95e+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 6.86e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.14e+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 6.14e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.87 -   105.67: 63
      105.67 -   111.47: 2421
      111.47 -   117.28: 571
      117.28 -   123.08: 809
      123.08 -   128.88: 215
  Bond angle restraints: 4079
  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  118.92    3.68 1.00e+00 1.00e+00 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  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  115.97   -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  126.89    4.31 1.30e+00 5.92e-01 1.10e+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  115.91   -3.31 1.00e+00 1.00e+00 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 957
       16.01 -    32.01: 53
       32.01 -    48.02: 18
       48.02 -    64.02: 3
       64.02 -    80.03: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.52   22.48     0      5.00e+00 4.00e-02 2.02e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.40   16.60     0      5.00e+00 4.00e-02 1.10e+01
  dihedral model="   0" pdb=" N   MET A 128 "
           model="   0" pdb=" CA  MET A 128 "
           model="   0" pdb=" CB  MET A 128 "
           model="   0" pdb=" CG  MET A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.31   51.31     3      1.50e+01 4.44e-03 9.00e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 76
       0.044 -    0.088: 47
       0.088 -    0.132: 36
       0.132 -    0.175: 14
       0.175 -    0.219: 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    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.95e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.068 2.00e-02 2.50e+03   2.93e-02 2.58e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.023 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 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.068 2.00e-02 2.50e+03   2.76e-02 2.28e+01
        model="   0" pdb=" CG  TYR A  81 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.023 2.00e-02 2.50e+03   4.69e-02 2.20e+01
        model="   0" pdb=" CG  ASP A  36 "    0.081 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.11: 71
        2.11 -     2.73: 3707
        2.73 -     3.35: 6270
        3.35 -     3.98: 7531
        3.98 -     4.60: 11403
  Nonbonded interactions: 28982
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.482 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.690 1.850
  nonbonded model="   0" pdb="HD11 LEU A  64 "
            model="   0" pdb=" HE3 LYS A 101 "
     model   vdw
     1.726 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.741 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.760 1.850
  ... (remaining 28977 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================

  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   9.02
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.56
  MolProbity score      =   1.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.97, per 1000 atoms: 0.44
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (62.189, 53.667, 67.726, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 1.25 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.12 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 104
        1.23 -     1.43: 368
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.13e+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 5.97e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.77e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.50e+00
  bond model="   0" pdb=" CB  THR A  82 "
       model="   0" pdb=" OG1 THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.433  1.396  0.037 1.60e-02 3.91e+03 5.29e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.27 -   106.02: 91
      106.02 -   111.77: 2481
      111.77 -   117.52: 494
      117.52 -   123.27: 818
      123.27 -   129.03: 195
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.50    4.10 1.00e+00 1.00e+00 1.68e+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  119.00    3.60 1.00e+00 1.00e+00 1.30e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.87    4.33 1.30e+00 5.92e-01 1.11e+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  129.03   -4.63 1.40e+00 5.10e-01 1.09e+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  127.05    4.15 1.30e+00 5.92e-01 1.02e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 968
       17.89 -    35.77: 45
       35.77 -    53.66: 16
       53.66 -    71.55: 3
       71.55 -    89.43: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.51   23.49     0      5.00e+00 4.00e-02 2.21e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.08   18.92     0      5.00e+00 4.00e-02 1.43e+01
  dihedral model="   0" pdb=" CA  GLY A  96 "
           model="   0" pdb=" C   GLY A  96 "
           model="   0" pdb=" N   SER A  97 "
           model="   0" pdb=" CA  SER A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.90   17.10     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 69
       0.040 -    0.080: 45
       0.080 -    0.120: 40
       0.120 -    0.160: 19
       0.160 -    0.200: 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 1.00e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.21e-01
  chirality model="   0" pdb=" CA  SER A  97 "
            model="   0" pdb=" N   SER A  97 "
            model="   0" pdb=" C   SER A  97 "
            model="   0" pdb=" CB  SER A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.42e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "    0.123 2.00e-02 2.50e+03   4.90e-02 7.21e+01
        model="   0" pdb=" CG  PHE A  15 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "    0.064 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.072 2.00e-02 2.50e+03   3.12e-02 2.92e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.062 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.019 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   1.95e-02 1.14e+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 "   -0.012 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 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 122
        2.15 -     2.76: 4071
        2.76 -     3.37: 6261
        3.37 -     3.99: 7636
        3.99 -     4.60: 11488
  Nonbonded interactions: 29578
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   THR A  82 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     1.536 2.620
  nonbonded model="   0" pdb="HD21 LEU A  93 "
            model="   0" pdb=" HB2 LEU A  99 "
     model   vdw
     1.579 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.706 1.850
  nonbonded model="   0" pdb="HG23 THR A  83 "
            model="   0" pdb=" HA  THR A  92 "
     model   vdw
     1.709 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.741 1.850
  ... (remaining 29573 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.714, 62.377, 61.903, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.156, 64.591, 61.705, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 6
        1.23 -     1.42: 459
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.389 -0.015 1.10e-02 8.26e+03 1.86e+00
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.82e+00
  bond model="   0" pdb=" C   LYS A 125 "
       model="   0" pdb=" N   VAL A 126 "
    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   HIS A 135 "
       model="   0" pdb=" N   HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.28e+00
  bond model="   0" pdb=" C   TYR A  81 "
       model="   0" pdb=" N   THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.015 1.40e-02 5.10e+03 1.20e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.62 -   106.70: 59
      106.70 -   112.78: 2708
      112.78 -   118.86: 439
      118.86 -   124.94: 831
      124.94 -   131.03: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.96   -4.96 3.00e+00 1.11e-01 2.73e+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  104.33    4.67 3.00e+00 1.11e-01 2.42e+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  105.39    4.61 3.00e+00 1.11e-01 2.36e+00
  angle model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" CB  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     111.60  108.57    3.03 2.00e+00 2.50e-01 2.30e+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  105.50    4.50 3.00e+00 1.11e-01 2.25e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 993
       16.49 -    32.97: 18
       32.97 -    49.46: 11
       49.46 -    65.94: 6
       65.94 -    82.43: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   82.43  -82.43     1      3.00e+01 1.11e-03 9.26e+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  -76.51   76.51     1      3.00e+01 1.11e-03 8.18e+00
  dihedral model="   0" pdb=" CA  ASP A  47 "
           model="   0" pdb=" CB  ASP A  47 "
           model="   0" pdb=" CG  ASP A  47 "
           model="   0" pdb=" OD1 ASP A  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -74.52   44.52     1      2.00e+01 2.50e-03 6.89e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 100
       0.030 -    0.061: 57
       0.061 -    0.091: 7
       0.091 -    0.121: 6
       0.121 -    0.152: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.74e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.34e-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    2.58   -0.15 2.00e-01 2.50e+01 5.28e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.015 5.00e-02 4.00e+02   2.32e-02 8.61e-01
        model="   0" pdb=" N   PRO A   6 "   -0.040 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.013 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.011 2.00e-02 2.50e+03   5.07e-03 7.70e-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 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.002 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 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "    0.011 2.00e-02 2.50e+03   4.23e-03 5.36e-01
        model="   0" pdb=" CG  TYR A  68 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 210
        2.25 -     2.83: 5026
        2.83 -     3.42: 5523
        3.42 -     4.01: 7375
        4.01 -     4.60: 10851
  Nonbonded interactions: 28985
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A  32 "
            model="   0" pdb="HD21 ASN A  72 "
     model   vdw
     1.658 1.850
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" O   ASP A  44 "
     model   vdw
     1.799 2.620
  nonbonded model="   0" pdb=" HZ1 LYS A  63 "
            model="   0" pdb=" HD1 TYR A  89 "
     model   vdw
     1.802 2.100
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.843 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.847 2.270
  ... (remaining 28980 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.972, 56.353, 44.229, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.11 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.67
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.76 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 0.86, per 1000 atoms: 0.39
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.912, 52.923, 53.201, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 13
        1.23 -     1.42: 458
        1.42 -     1.62: 661
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.342 -0.021 1.00e-02 1.00e+04 4.46e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.340 -0.019 1.00e-02 1.00e+04 3.44e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.338 -0.017 1.00e-02 1.00e+04 2.92e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.338 -0.017 1.00e-02 1.00e+04 2.79e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.37e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.45 -   106.29: 63
      106.29 -   112.13: 2625
      112.13 -   117.96: 443
      117.96 -   123.80: 871
      123.80 -   129.64: 77
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   HIS A 138 "
        model="   0" pdb=" N   HIS A 139 "
        model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     121.70  128.62   -6.92 1.80e+00 3.09e-01 1.48e+01
  angle model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" CA  HIS A 139 "
        model="   0" pdb=" HA  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     109.00  102.45    6.55 3.00e+00 1.11e-01 4.77e+00
  angle model="   0" pdb=" N   HIS A 139 "
        model="   0" pdb=" CA  HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
      ideal   model   delta    sigma   weight residual
     111.00  117.07   -6.07 2.80e+00 1.28e-01 4.70e+00
  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  125.49   -3.79 1.80e+00 3.09e-01 4.44e+00
  angle model="   0" pdb=" N   HIS A 139 "
        model="   0" pdb=" CA  HIS A 139 "
        model="   0" pdb=" HA  HIS A 139 "
      ideal   model   delta    sigma   weight residual
     110.00  103.86    6.14 3.00e+00 1.11e-01 4.19e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 998
       17.66 -    35.32: 21
       35.32 -    52.98: 7
       52.98 -    70.65: 4
       70.65 -    88.31: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
           model="   0" pdb=" CD  GLU A  55 "
           model="   0" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.14   82.14     1      3.00e+01 1.11e-03 9.21e+00
  dihedral model="   0" pdb=" C   HIS A 139 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
           model="   0" pdb=" CB  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -129.96    7.36     0      2.50e+00 1.60e-01 8.67e+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   76.26  -76.26     1      3.00e+01 1.11e-03 8.13e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 119
       0.051 -    0.102: 48
       0.102 -    0.152: 7
       0.152 -    0.203: 1
       0.203 -    0.254: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 139 "
            model="   0" pdb=" N   HIS A 139 "
            model="   0" pdb=" C   HIS A 139 "
            model="   0" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+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    2.60   -0.16 2.00e-01 2.50e+01 6.76e-01
  chirality model="   0" pdb=" CA  PRO A 114 "
            model="   0" pdb=" N   PRO A 114 "
            model="   0" pdb=" C   PRO A 114 "
            model="   0" pdb=" CB  PRO A 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.38e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.036 2.00e-02 2.50e+03   1.43e-02 6.10e+00
        model="   0" pdb=" CG  TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.007 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 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.009 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 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.029 2.00e-02 2.50e+03   1.10e-02 3.64e+00
        model="   0" pdb=" CG  TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.016 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 "    0.011 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=" CB  TYR A  91 "   -0.026 2.00e-02 2.50e+03   1.01e-02 3.04e+00
        model="   0" pdb=" CG  TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 131
        2.18 -     2.79: 4347
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        2.79 -     3.39: 6085
        3.39 -     4.00: 7539
        4.00 -     4.60: 11452
  Nonbonded interactions: 29554
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  38 "
            model="   0" pdb="HG21 ILE A 122 "
     model   vdw
     1.579 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.769 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.799 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.822 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.825 1.850
  ... (remaining 29549 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.22, per 1000 atoms: 0.55
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.78, 58.778, 49.204, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 66
        1.23 -     1.42: 406
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.57e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 6.00e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.40e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.302  0.028 1.30e-02 5.92e+03 4.63e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.377 -0.023 1.10e-02 8.26e+03 4.54e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.61 -   106.23: 86
      106.23 -   111.85: 2538
      111.85 -   117.47: 447
      117.47 -   123.09: 794
      123.09 -   128.71: 214
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.16    3.44 1.00e+00 1.00e+00 1.18e+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  126.88    4.32 1.30e+00 5.92e-01 1.10e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  127.07    4.13 1.30e+00 5.92e-01 1.01e+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  119.50    3.10 1.00e+00 1.00e+00 9.60e+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  115.62   -3.02 1.00e+00 1.00e+00 9.14e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 980
       17.60 -    35.20: 37
       35.20 -    52.80: 10
       52.80 -    70.39: 2
       70.39 -    87.99: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LEU A  93 "
           model="   0" pdb=" C   LEU A  93 "
           model="   0" pdb=" N   GLY A  94 "
           model="   0" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.13  -23.87     0      5.00e+00 4.00e-02 2.28e+01
  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  -86.39   86.39     1      3.00e+01 1.11e-03 9.99e+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   81.82  -81.82     1      3.00e+01 1.11e-03 9.15e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.035: 72
       0.035 -    0.070: 49
       0.070 -    0.104: 30
       0.104 -    0.138: 20
       0.138 -    0.173: 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    2.34    0.17 2.00e-01 2.50e+01 7.48e-01
  chirality model="   0" pdb=" CB  THR A  92 "
            model="   0" pdb=" CA  THR A  92 "
            model="   0" pdb=" OG1 THR A  92 "
            model="   0" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.15 2.00e-01 2.50e+01 5.30e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.09e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.059 2.00e-02 2.50e+03   2.27e-02 1.55e+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 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 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 "    0.035 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 "   -0.022 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  50 "   -0.052 2.00e-02 2.50e+03   2.19e-02 1.44e+01
        model="   0" pdb=" CG  TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.044 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 "    0.015 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 "    0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CG  GLU A 123 "    0.009 2.00e-02 2.50e+03   1.89e-02 3.56e+00
        model="   0" pdb=" CD  GLU A 123 "   -0.033 2.00e-02 2.50e+03
        model="   0" pdb=" OE1 GLU A 123 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" OE2 GLU A 123 "    0.012 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.77 -     2.34: 465
        2.34 -     2.90: 5084
        2.90 -     3.47: 5247
        3.47 -     4.03: 6785
        4.03 -     4.60: 9989
  Nonbonded interactions: 27570
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.769 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A 113 "
            model="   0" pdb=" OE1 GLU A 120 "
     model   vdw
     1.771 1.850
  nonbonded model="   0" pdb=" OE1 GLU A  75 "
            model="   0" pdb=" HZ1 LYS A  79 "
     model   vdw
     1.814 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.821 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A 109 "
            model="   0" pdb=" OD1 ASP A 110 "
     model   vdw
     1.850 1.850
  ... (remaining 27565 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 1
        1.22 -     1.42: 462
        1.42 -     1.61: 669
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.194  0.037 2.00e-02 2.50e+03 3.41e+00
  bond model="   0" pdb=" C   ASP A  74 "
       model="   0" pdb=" N   GLU A  75 "
    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   PRO A 117 "
       model="   0" pdb=" N   ASP A 118 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.57e+00
  bond model="   0" pdb=" C   TYR A 111 "
       model="   0" pdb=" N   VAL A 112 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.50e+00
  bond model="   0" pdb=" C   TYR A  81 "
       model="   0" pdb=" N   THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 1.96e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.39 -   106.49: 44
      106.49 -   112.59: 2740
      112.59 -   118.70: 417
      118.70 -   124.80: 833
      124.80 -   130.90: 45
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.96   -4.96 3.00e+00 1.11e-01 2.73e+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  113.40   -4.40 3.00e+00 1.11e-01 2.15e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.38   -4.38 3.00e+00 1.11e-01 2.13e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.25   -4.25 3.00e+00 1.11e-01 2.01e+00
  angle model="   0" pdb=" CA  HIS A 138 "
        model="   0" pdb=" CB  HIS A 138 "
        model="   0" pdb=" CG  HIS A 138 "
      ideal   model   delta    sigma   weight residual
     113.80  112.40    1.40 1.00e+00 1.00e+00 1.97e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 1006
       17.79 -    35.57: 10
       35.57 -    53.36: 11
       53.36 -    71.15: 4
       71.15 -    88.93: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CE1 TYR A  91 "
           model="   0" pdb=" CZ  TYR A  91 "
           model="   0" pdb=" OH  TYR A  91 "
           model="   0" pdb=" HH  TYR A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.93  -88.93     2      3.00e+01 1.11e-03 5.33e+00
  dihedral model="   0" pdb=" CB  GLN A  28 "
           model="   0" pdb=" CG  GLN A  28 "
           model="   0" pdb=" CD  GLN A  28 "
           model="   0" pdb=" OE1 GLN A  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   75.43  -75.43     2      3.00e+01 1.11e-03 5.00e+00
  dihedral model="   0" pdb=" CB  GLN A 100 "
           model="   0" pdb=" CG  GLN A 100 "
           model="   0" pdb=" CD  GLN A 100 "
           model="   0" pdb=" OE1 GLN A 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -70.47   70.47     2      3.00e+01 1.11e-03 4.74e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 106
       0.025 -    0.051: 49
       0.051 -    0.076: 6
       0.076 -    0.101: 10
       0.101 -    0.126: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.07e-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   -0.11 2.00e-01 2.50e+01 2.83e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.010 2.00e-02 2.50e+03   4.07e-03 4.96e-01
        model="   0" pdb=" CG  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.007 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 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.001 2.00e-02 2.50e+03   3.84e-03 4.42e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.002 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 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 "   -0.007 2.00e-02 2.50e+03   4.47e-03 3.99e-01
        model="   0" pdb=" CG  HIS A 139 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.24 -     1.91: 14
        1.91 -     2.58: 2306
        2.58 -     3.26: 6714
        3.26 -     3.93: 7868
        3.93 -     4.60: 12406
  Nonbonded interactions: 29308
  Sorted by model distance:
  nonbonded model="   0" pdb="HG12 ILE A  86 "
            model="   0" pdb=" HE1 TYR A  91 "
     model   vdw
     1.241 2.270
  nonbonded model="   0" pdb=" HB3 ASP A  47 "
            model="   0" pdb=" HD2 TYR A  50 "
     model   vdw
     1.651 2.270
  nonbonded model="   0" pdb=" O   LYS A  79 "
            model="   0" pdb=" HA2 GLY A  96 "
     model   vdw
     1.679 2.620
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.680 2.270
  nonbonded model="   0" pdb="HD12 ILE A  37 "
            model="   0" pdb="HD23 LEU A  61 "
     model   vdw
     1.719 2.440
  ... (remaining 29303 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 92
        1.23 -     1.43: 380
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.33e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.03e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.99e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.75e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.15e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.56 -   106.27: 113
      106.27 -   111.98: 2521
      111.98 -   117.68: 451
      117.68 -   123.39: 829
      123.39 -   129.10: 165
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.10   -3.50 1.00e+00 1.00e+00 1.22e+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  126.68    4.52 1.30e+00 5.92e-01 1.21e+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  119.24    3.36 1.00e+00 1.00e+00 1.13e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.10   -4.70 1.40e+00 5.10e-01 1.13e+01
  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  119.37    3.23 1.00e+00 1.00e+00 1.04e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 968
       17.51 -    35.01: 47
       35.01 -    52.52: 12
       52.52 -    70.03: 5
       70.03 -    87.54: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.84   20.16     0      5.00e+00 4.00e-02 1.63e+01
  dihedral model="   0" pdb=" N   ARG A 129 "
           model="   0" pdb=" CA  ARG A 129 "
           model="   0" pdb=" CB  ARG A 129 "
           model="   0" pdb=" CG  ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -123.69  -56.31     3      1.50e+01 4.44e-03 9.39e+00
  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  164.71   15.29     0      5.00e+00 4.00e-02 9.35e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 67
       0.035 -    0.070: 40
       0.070 -    0.104: 39
       0.104 -    0.139: 23
       0.139 -    0.174: 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    2.34    0.17 2.00e-01 2.50e+01 7.57e-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 6.39e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.91e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.063 2.00e-02 2.50e+03   2.78e-02 2.32e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.020 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 "   -0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.057 2.00e-02 2.50e+03   2.24e-02 1.51e+01
        model="   0" pdb=" CG  TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.006 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 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.017 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 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.047 2.00e-02 2.50e+03   1.84e-02 1.01e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 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 "    0.031 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 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 58
        2.08 -     2.71: 3523
        2.71 -     3.34: 6255
        3.34 -     3.97: 7432
        3.97 -     4.60: 11281
  Nonbonded interactions: 28549
  Sorted by model distance:
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" HE2 TYR A  81 "
     model   vdw
     1.451 2.270
  nonbonded model="   0" pdb=" HB2 SER A  46 "
            model="   0" pdb="HH12 ARG A 129 "
     model   vdw
     1.639 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.683 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=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.752 1.850
  ... (remaining 28544 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.65, per 1000 atoms: 0.29
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.005, 67.096, 59.953, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.98 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.92 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 58
        1.23 -     1.42: 414
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.68e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.11e+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 6.44e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.74e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.46e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.26 -   106.02: 85
      106.02 -   111.77: 2504
      111.77 -   117.53: 482
      117.53 -   123.28: 818
      123.28 -   129.04: 190
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.57    4.03 1.00e+00 1.00e+00 1.62e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.29   -3.69 1.00e+00 1.00e+00 1.36e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.48    4.72 1.30e+00 5.92e-01 1.32e+01
  angle model="   0" pdb=" 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  126.56    4.64 1.30e+00 5.92e-01 1.27e+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  116.11   -3.51 1.00e+00 1.00e+00 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.29: 961
       16.29 -    32.58: 45
       32.58 -    48.88: 15
       48.88 -    65.17: 9
       65.17 -    81.46: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.73   23.27     0      5.00e+00 4.00e-02 2.17e+01
  dihedral model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
           model="   0" pdb=" CB  HIS A 139 "
           model="   0" pdb=" CG  HIS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.83  -58.17     3      1.50e+01 4.44e-03 9.46e+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  164.63   15.37     0      5.00e+00 4.00e-02 9.45e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 71
       0.040 -    0.080: 45
       0.080 -    0.120: 38
       0.120 -    0.160: 18
       0.160 -    0.200: 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    2.31    0.20 2.00e-01 2.50e+01 9.99e-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 8.28e-01
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.44e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.149 2.00e-02 2.50e+03   6.38e-02 1.22e+02
        model="   0" pdb=" CG  TYR A  81 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.123 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.033 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.022 2.00e-02 2.50e+03   4.54e-02 2.06e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.079 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.058 2.00e-02 2.50e+03   2.62e-02 2.06e+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 "   -0.012 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 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 112
        2.15 -     2.76: 4093
        2.76 -     3.37: 6248
        3.37 -     3.99: 7566
        3.99 -     4.60: 11382
  Nonbonded interactions: 29401
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.537 1.850
  nonbonded model="   0" pdb=" HD1 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.555 2.270
  nonbonded model="   0" pdb="HG23 ILE A  78 "
            model="   0" pdb="HD22 LEU A  93 "
     model   vdw
     1.606 2.440
  nonbonded model="   0" pdb=" HB2 TYR A  81 "
            model="   0" pdb="HD13 LEU A  93 "
     model   vdw
     1.687 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.705 1.850
  ... (remaining 29396 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: 108
        1.23 -     1.43: 364
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.11e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.08e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.61e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.44e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.88e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.08 -   105.05: 46
      105.05 -   111.03: 2328
      111.03 -   117.01: 668
      117.01 -   122.99: 802
      122.99 -   128.97: 235
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   THR A  82 "
        model="   0" pdb=" CA  THR A  82 "
        model="   0" pdb=" CB  THR A  82 "
      ideal   model   delta    sigma   weight residual
     111.50  118.22   -6.72 1.70e+00 3.46e-01 1.56e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.68    3.92 1.00e+00 1.00e+00 1.53e+01
  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   99.08   10.92 3.00e+00 1.11e-01 1.33e+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  126.52    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  119.23    3.37 1.00e+00 1.00e+00 1.13e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 963
       17.81 -    35.61: 45
       35.61 -    53.42: 19
       53.42 -    71.22: 5
       71.22 -    89.03: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.48   19.52     0      5.00e+00 4.00e-02 1.52e+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  161.30   18.70     0      5.00e+00 4.00e-02 1.40e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.18   16.82     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 76
       0.053 -    0.105: 61
       0.105 -    0.158: 31
       0.158 -    0.211: 6
       0.211 -    0.263: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CB  THR A  82 "
            model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" OG1 THR A  82 "
            model="   0" pdb=" CG2 THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.066 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 "   -0.015 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 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.058 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 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.014 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   2.22e-02 1.48e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 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 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 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 9.42e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.003 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 "    0.028 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
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.36 -     2.01: 30
        2.01 -     2.66: 2908
        2.66 -     3.30: 6446
        3.30 -     3.95: 7672
        3.95 -     4.60: 11555
  Nonbonded interactions: 28611
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb="HG13 ILE A  77 "
     model   vdw
     1.359 2.620
  nonbonded model="   0" pdb=" HG  SER A  17 "
            model="   0" pdb=" OE2 GLU A  84 "
     model   vdw
     1.525 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.636 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.683 1.850
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" OE1 GLU A  84 "
     model   vdw
     1.750 2.450
  ... (remaining 28606 not shown)

  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: 111
        1.23 -     1.43: 361
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.80e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.14e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.34e+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 6.69e+00
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.36e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.95 -   105.76: 75
      105.76 -   111.57: 2433
      111.57 -   117.38: 552
      117.38 -   123.19: 818
      123.19 -   129.00: 201
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.73    3.87 1.00e+00 1.00e+00 1.49e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.60    4.60 1.30e+00 5.92e-01 1.25e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.15    3.45 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.00   -4.60 1.40e+00 5.10e-01 1.08e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.81   -3.21 1.00e+00 1.00e+00 1.03e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 966
       17.85 -    35.70: 44
       35.70 -    53.55: 16
       53.55 -    71.39: 6
       71.39 -    89.24: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.73   38.27     0      5.00e+00 4.00e-02 5.86e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.55   22.45     0      5.00e+00 4.00e-02 2.02e+01
  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  160.37   19.63     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 75
       0.046 -    0.090: 52
       0.090 -    0.135: 33
       0.135 -    0.180: 11
       0.180 -    0.224: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.058 2.00e-02 2.50e+03   2.46e-02 1.82e+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 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.021 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 "   -0.013 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   2.41e-02 1.75e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  LEU A  93 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        model="   0" pdb=" C   LEU A  93 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" O   LEU A  93 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" N   GLY A  94 "    0.020 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.17: 125
        2.17 -     2.78: 4213
        2.78 -     3.39: 6125
        3.39 -     3.99: 7333
        3.99 -     4.60: 11105
  Nonbonded interactions: 28901
  Sorted by model distance:
  nonbonded model="   0" pdb="HD23 LEU A 119 "
            model="   0" pdb="HD12 ILE A 122 "
     model   vdw
     1.568 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.680 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.738 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A 109 "
            model="   0" pdb=" OD1 ASP A 110 "
     model   vdw
     1.750 1.850
  ... (remaining 28896 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: 61
        1.23 -     1.42: 411
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 8.87e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.45e+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 6.43e+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 6.27e+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 6.22e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.79 -   105.62: 58
      105.62 -   111.45: 2424
      111.45 -   117.27: 577
      117.27 -   123.10: 798
      123.10 -   128.93: 222
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.36    4.24 1.00e+00 1.00e+00 1.80e+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  126.07    5.13 1.30e+00 5.92e-01 1.55e+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  126.51    4.69 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  119.10    3.50 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.93   -4.53 1.40e+00 5.10e-01 1.05e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 979
       17.80 -    35.60: 36
       35.60 -    53.40: 16
       53.40 -    71.19: 1
       71.19 -    88.99: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.29   27.71     0      5.00e+00 4.00e-02 3.07e+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  152.74   27.26     0      5.00e+00 4.00e-02 2.97e+01
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.81   25.19     0      5.00e+00 4.00e-02 2.54e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 70
       0.038 -    0.077: 43
       0.077 -    0.115: 40
       0.115 -    0.153: 21
       0.153 -    0.192: 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    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.52e-01
  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   -2.74    0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.025 2.00e-02 2.50e+03   5.07e-02 2.57e+01
        model="   0" pdb=" CG  ASP A  36 "    0.088 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.031 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.059 2.00e-02 2.50e+03   2.53e-02 1.92e+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 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.051 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 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 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   2.44e-02 1.78e+01
        model="   0" pdb=" CG  TYR A 111 "    0.012 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 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 104
        2.13 -     2.75: 3936
        2.75 -     3.37: 6053
        3.37 -     3.98: 7611
        3.98 -     4.60: 11256
  Nonbonded interactions: 28960
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.514 1.850
  nonbonded model="   0" pdb=" HG  SER A  76 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.578 2.100
  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  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.709 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.731 1.850
  ... (remaining 28955 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU   49": "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"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 2
        1.23 -     1.42: 463
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   TYR A  89 "
       model="   0" pdb=" N   SER A  90 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.92e+00
  bond model="   0" pdb=" C   ARG A 129 "
       model="   0" pdb=" N   SER A 130 "
    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=" C   HIS A 135 "
       model="   0" pdb=" N   HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.59e+00
  bond model="   0" pdb=" C   GLU A 133 "
       model="   0" pdb=" N   HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.50e+00
  bond model="   0" pdb=" C   HIS A 136 "
       model="   0" pdb=" N   HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.48e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.56 -   106.63: 49
      106.63 -   112.70: 2721
      112.70 -   118.77: 433
      118.77 -   124.84: 832
      124.84 -   130.91: 44
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.02   -5.02 3.00e+00 1.11e-01 2.80e+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  104.02    4.98 3.00e+00 1.11e-01 2.76e+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  104.14    4.86 3.00e+00 1.11e-01 2.62e+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  113.80   -4.80 3.00e+00 1.11e-01 2.56e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.48   -4.48 3.00e+00 1.11e-01 2.23e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.86: 1006
       15.86 -    31.72: 14
       31.72 -    47.58: 11
       47.58 -    63.44: 0
       63.44 -    79.30: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CE1 TYR A  50 "
           model="   0" pdb=" CZ  TYR A  50 "
           model="   0" pdb=" OH  TYR A  50 "
           model="   0" pdb=" HH  TYR A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  100.70   79.30     2      3.00e+01 1.11e-03 5.15e+00
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -105.42  -74.58     2      3.00e+01 1.11e-03 4.96e+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   39.97  -39.97     1      3.00e+01 1.11e-03 2.49e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 119
       0.029 -    0.058: 40
       0.058 -    0.087: 10
       0.087 -    0.115: 5
       0.115 -    0.144: 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   -0.14 2.00e-01 2.50e+01 5.20e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.82e-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 2.92e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.014 5.00e-02 4.00e+02   2.08e-02 6.90e-01
        model="   0" pdb=" N   PRO A   6 "   -0.036 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=" CA  HIS A 139 "   -0.004 2.00e-02 2.50e+03   8.02e-03 6.43e-01
        model="   0" pdb=" C   HIS A 139 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" O   HIS A 139 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OXT HIS A 139 "   -0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "    0.012 5.00e-02 4.00e+02   1.80e-02 5.18e-01
        model="   0" pdb=" N   PRO A  54 "   -0.031 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "    0.009 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "    0.010 5.00e-02 4.00e+02
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 151
        2.21 -     2.81: 4634
        2.81 -     3.40: 5606
        3.40 -     4.00: 7160
        4.00 -     4.60: 10634
  Nonbonded interactions: 28185
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   VAL A  41 "
            model="   0" pdb=" H   LYS A 113 "
     model   vdw
     1.609 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.775 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.793 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  29 "
            model="   0" pdb="HD22 ASN A  72 "
     model   vdw
     1.800 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.844 1.850
  ... (remaining 28180 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (39.573, 54.984, 70.573, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.212, 64.767, 60.232, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.71
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.78 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 68
        1.23 -     1.43: 404
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.59e+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 6.95e+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 6.86e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.14e+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 6.14e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.87 -   105.67: 63
      105.67 -   111.47: 2421
      111.47 -   117.28: 571
      117.28 -   123.08: 809
      123.08 -   128.88: 215
  Bond angle restraints: 4079
  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  118.92    3.68 1.00e+00 1.00e+00 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  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  115.97   -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  126.89    4.31 1.30e+00 5.92e-01 1.10e+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  115.91   -3.31 1.00e+00 1.00e+00 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 957
       16.01 -    32.01: 53
       32.01 -    48.02: 18
       48.02 -    64.02: 3
       64.02 -    80.03: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.52   22.48     0      5.00e+00 4.00e-02 2.02e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.40   16.60     0      5.00e+00 4.00e-02 1.10e+01
  dihedral model="   0" pdb=" N   MET A 128 "
           model="   0" pdb=" CA  MET A 128 "
           model="   0" pdb=" CB  MET A 128 "
           model="   0" pdb=" CG  MET A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -111.31   51.31     3      1.50e+01 4.44e-03 9.00e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 76
       0.044 -    0.088: 47
       0.088 -    0.132: 36
       0.132 -    0.175: 14
       0.175 -    0.219: 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    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality model="   0" pdb=" CA  HIS A 137 "
            model="   0" pdb=" N   HIS A 137 "
            model="   0" pdb=" C   HIS A 137 "
            model="   0" pdb=" CB  HIS A 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.95e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.068 2.00e-02 2.50e+03   2.93e-02 2.58e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.023 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 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.068 2.00e-02 2.50e+03   2.76e-02 2.28e+01
        model="   0" pdb=" CG  TYR A  81 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.011 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.023 2.00e-02 2.50e+03   4.69e-02 2.20e+01
        model="   0" pdb=" CG  ASP A  36 "    0.081 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.11: 71
        2.11 -     2.73: 3707
        2.73 -     3.35: 6270
        3.35 -     3.98: 7531
        3.98 -     4.60: 11403
  Nonbonded interactions: 28982
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.482 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.690 1.850
  nonbonded model="   0" pdb="HD11 LEU A  64 "
            model="   0" pdb=" HE3 LYS A 101 "
     model   vdw
     1.726 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.741 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.760 1.850
  ... (remaining 28977 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: 669
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   VAL A 126 "
       model="   0" pdb=" N   ARG A 127 "
    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=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.389 -0.015 1.10e-02 8.26e+03 1.88e+00
  bond model="   0" pdb=" C   ARG A 127 "
       model="   0" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.53e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.309  0.012 1.00e-02 1.00e+04 1.51e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.28 -   106.50: 55
      106.50 -   112.72: 2700
      112.72 -   118.94: 452
      118.94 -   125.16: 829
      125.16 -   131.37: 43
  Bond angle restraints: 4079
  Sorted by residual:
  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  105.14    4.86 3.00e+00 1.11e-01 2.62e+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  104.15    4.85 3.00e+00 1.11e-01 2.61e+00
  angle model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" CB  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     111.60  108.37    3.23 2.00e+00 2.50e-01 2.61e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  105.35    4.65 3.00e+00 1.11e-01 2.41e+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  113.56   -4.56 3.00e+00 1.11e-01 2.31e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 978
       17.12 -    34.24: 27
       34.24 -    51.35: 12
       51.35 -    68.47: 8
       68.47 -    85.59: 8
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
           model="   0" pdb=" CD  GLU A  55 "
           model="   0" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.59  -85.59     1      3.00e+01 1.11e-03 9.85e+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  -78.08   78.08     1      3.00e+01 1.11e-03 8.46e+00
  dihedral model="   0" pdb=" CB  GLU A  75 "
           model="   0" pdb=" CG  GLU A  75 "
           model="   0" pdb=" CD  GLU A  75 "
           model="   0" pdb=" OE1 GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   76.67  -76.67     1      3.00e+01 1.11e-03 8.21e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 105
       0.034 -    0.067: 51
       0.067 -    0.100: 9
       0.100 -    0.134: 8
       0.134 -    0.167: 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    2.60   -0.17 2.00e-01 2.50e+01 6.97e-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 6.10e-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    2.59   -0.15 2.00e-01 2.50e+01 5.95e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.018 2.00e-02 2.50e+03   6.78e-03 1.38e+00
        model="   0" pdb=" CG  TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.015 2.00e-02 2.50e+03   5.87e-03 1.04e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.004 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 "   -0.000 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 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.007 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 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.014 2.00e-02 2.50e+03   5.44e-03 8.88e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.007 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 "    0.002 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 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.10: 78
        2.10 -     2.72: 3995
        2.72 -     3.35: 6177
        3.35 -     3.97: 7742
        3.97 -     4.60: 11966
  Nonbonded interactions: 29958
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.474 1.850
  nonbonded model="   0" pdb="HG22 ILE A  71 "
            model="   0" pdb="HD11 ILE A  78 "
     model   vdw
     1.576 2.440
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" OH  TYR A  89 "
     model   vdw
     1.628 1.850
  nonbonded model="   0" pdb=" O   VAL A  41 "
            model="   0" pdb=" H   LYS A 113 "
     model   vdw
     1.686 1.850
  nonbonded model="   0" pdb=" HE  ARG A  21 "
            model="   0" pdb=" OD2 ASP A  29 "
     model   vdw
     1.729 1.850
  ... (remaining 29953 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 71
        1.23 -     1.42: 401
        1.42 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.08e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.41e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.28e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.11e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.80e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       97.50 -   103.80: 17
      103.80 -   110.09: 2136
      110.09 -   116.38: 873
      116.38 -   122.67: 750
      122.67 -   128.97: 303
  Bond angle restraints: 4079
  Sorted by residual:
  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  126.01    5.19 1.30e+00 5.92e-01 1.59e+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  118.62    3.98 1.00e+00 1.00e+00 1.58e+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  126.66    4.54 1.30e+00 5.92e-01 1.22e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.13    3.47 1.00e+00 1.00e+00 1.20e+01
  angle model="   0" pdb=" CA  HIS A 136 "
        model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
      ideal   model   delta    sigma   weight residual
     113.80  110.45    3.35 1.00e+00 1.00e+00 1.12e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 966
       17.57 -    35.15: 49
       35.15 -    52.72: 11
       52.72 -    70.30: 3
       70.30 -    87.87: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A 123 "
           model="   0" pdb=" C   GLU A 123 "
           model="   0" pdb=" N   ALA A 124 "
           model="   0" pdb=" CA  ALA A 124 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.80   31.20     0      5.00e+00 4.00e-02 3.89e+01
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.06   24.94     0      5.00e+00 4.00e-02 2.49e+01
  dihedral model="   0" pdb=" CA  ILE A 122 "
           model="   0" pdb=" C   ILE A 122 "
           model="   0" pdb=" N   GLU A 123 "
           model="   0" pdb=" CA  GLU A 123 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.64   24.36     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 75
       0.050 -    0.099: 64
       0.099 -    0.148: 30
       0.148 -    0.197: 5
       0.197 -    0.246: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 136 "
            model="   0" pdb=" N   HIS A 136 "
            model="   0" pdb=" C   HIS A 136 "
            model="   0" pdb=" CB  HIS A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.51e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.35e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.073 2.00e-02 2.50e+03   3.23e-02 3.14e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.066 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 "   -0.025 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 "   -0.020 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   2.38e-02 1.70e+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 "    0.014 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 105 "    0.047 2.00e-02 2.50e+03   1.82e-02 9.89e+00
        model="   0" pdb=" CG  TYR A 105 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 105 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 105 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 105 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 105 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 105 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 105 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 105 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 105 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 105 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 105 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 157
        2.19 -     2.79: 4357
        2.79 -     3.40: 6057
        3.40 -     4.00: 7300
        4.00 -     4.60: 11174
  Nonbonded interactions: 29045
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.589 1.850
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" OE1 GLU A  84 "
     model   vdw
     1.590 2.450
  nonbonded model="   0" pdb="HD21 LEU A  39 "
            model="   0" pdb="HG21 VAL A 126 "
     model   vdw
     1.610 2.440
  nonbonded model="   0" pdb=" HG  LEU A  39 "
            model="   0" pdb=" HE2 MET A 128 "
     model   vdw
     1.655 2.440
  nonbonded model="   0" pdb=" HZ2 LYS A 109 "
            model="   0" pdb=" OD1 ASP A 110 "
     model   vdw
     1.707 1.850
  ... (remaining 29040 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: 130
        1.23 -     1.43: 342
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.30e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.19e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.03e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.60e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.29e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.65 -   106.29: 114
      106.29 -   111.92: 2497
      111.92 -   117.56: 459
      117.56 -   123.20: 806
      123.20 -   128.84: 203
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.47    4.13 1.00e+00 1.00e+00 1.71e+01
  angle model="   0" pdb=" CA  ASP A  44 "
        model="   0" pdb=" CB  ASP A  44 "
        model="   0" pdb=" CG  ASP A  44 "
      ideal   model   delta    sigma   weight residual
     112.60  116.58   -3.98 1.00e+00 1.00e+00 1.58e+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  126.29    4.91 1.30e+00 5.92e-01 1.42e+01
  angle model="   0" pdb=" C   SER A  97 "
        model="   0" pdb=" N   SER A  98 "
        model="   0" pdb=" CA  SER A  98 "
      ideal   model   delta    sigma   weight residual
     121.70  128.46   -6.76 1.80e+00 3.09e-01 1.41e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.25    3.35 1.00e+00 1.00e+00 1.12e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 959
       17.57 -    35.14: 57
       35.14 -    52.70: 11
       52.70 -    70.27: 4
       70.27 -    87.84: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.59   27.41     0      5.00e+00 4.00e-02 3.00e+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 -154.13  -25.87     0      5.00e+00 4.00e-02 2.68e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.47   25.53     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.055: 84
       0.055 -    0.110: 59
       0.110 -    0.164: 29
       0.164 -    0.218: 3
       0.218 -    0.273: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality model="   0" pdb=" CA  ASP A  74 "
            model="   0" pdb=" N   ASP A  74 "
            model="   0" pdb=" C   ASP A  74 "
            model="   0" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality model="   0" pdb=" 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: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.069 2.00e-02 2.50e+03   3.03e-02 2.75e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.052 2.00e-02 2.50e+03   2.04e-02 1.25e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 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 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.016 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
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.041 2.00e-02 2.50e+03   1.56e-02 7.26e+00
        model="   0" pdb=" CG  TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.020 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 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 117
        2.17 -     2.77: 4129
        2.77 -     3.38: 6069
        3.38 -     3.99: 7164
        3.99 -     4.60: 10968
  Nonbonded interactions: 28447
  Sorted by model distance:
  nonbonded model="   0" pdb="HD23 LEU A 119 "
            model="   0" pdb="HD12 ILE A 122 "
     model   vdw
     1.556 2.440
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.656 1.850
  nonbonded model="   0" pdb=" O   SER A  76 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.704 1.850
  nonbonded model="   0" pdb=" O   GLY A  96 "
            model="   0" pdb=" H   SER A  98 "
     model   vdw
     1.725 1.850
  nonbonded model="   0" pdb=" O   LYS A  79 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.740 1.850
  ... (remaining 28442 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (54.632, 41.726, 65.445, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.613, 46.794, 43.544, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.376, 45.029, 63.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.495)
  Mean delta:    0.012 (Z=  0.626)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    6.809 (Z=  3.844)
  Mean delta:    1.590 (Z=  0.865)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 114  PRO  CA
   A 114  PRO  C
   A 115  ALA  N
   A 115  ALA  CA        180.00   159.74    20.26  5.00e+00  1.64e+01   4.1*sigma

  Min. delta:    0.011
  Max. delta:   87.193
  Mean delta:   12.740

                       ----------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:    0.043
  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   0.039   2242  Z= 0.446
    Angle     :  1.532   6.809   4079  Z= 0.661
    Chirality :  0.075   0.194    176
    Planarity :  0.008   0.043    327
    Dihedral  : 12.157  87.193    769
    Min Nonbonded Distance : 1.291
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  1.61 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.66 (0.69), residues: 137
    helix:  0.44 (0.53), residues: 81
    sheet:  None (None), residues: 0
    loop :  0.72 (0.89), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 135 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.067   0.011   TYR A 111 
   ARG   0.035   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 135 
   PHE   0.007   0.003   PHE A  45 
   TYR   0.056   0.013   TYR A 111 
   ARG   0.004   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  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.

  Ramachandran outliers =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   4.51
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.53
  MolProbity score      =   1.82

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: 1.11
  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.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 69
        1.23 -     1.43: 403
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.83e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.57e+00
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.34e+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 7.26e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.18e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.38 -   106.33: 133
      106.33 -   112.28: 2545
      112.28 -   118.23: 444
      118.23 -   124.17: 861
      124.17 -   130.12: 96
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  130.12   -8.42 1.80e+00 3.09e-01 2.19e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.41    4.19 1.00e+00 1.00e+00 1.76e+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  125.79    5.41 1.30e+00 5.92e-01 1.73e+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  128.99   -7.29 1.80e+00 3.09e-01 1.64e+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 1.45e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 963
       17.98 -    35.97: 49
       35.97 -    53.95: 11
       53.95 -    71.93: 8
       71.93 -    89.91: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.82   30.18     0      5.00e+00 4.00e-02 3.64e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.66   28.34     0      5.00e+00 4.00e-02 3.21e+01
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.97  -27.03     0      5.00e+00 4.00e-02 2.92e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 79
       0.050 -    0.100: 54
       0.100 -    0.149: 34
       0.149 -    0.199: 5
       0.199 -    0.249: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality model="   0" pdb=" CA  TYR A  81 "
            model="   0" pdb=" N   TYR A  81 "
            model="   0" pdb=" C   TYR A  81 "
            model="   0" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.052 2.00e-02 2.50e+03   2.18e-02 1.42e+01
        model="   0" pdb=" CG  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.011 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 "    0.055 2.00e-02 2.50e+03   2.15e-02 1.38e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 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 "   -0.020 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 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  67 "    0.041 2.00e-02 2.50e+03   1.76e-02 9.29e+00
        model="   0" pdb=" CG  PHE A  67 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  67 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  67 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  67 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  67 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  67 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  67 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  67 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  67 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  67 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  67 "    0.027 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 205
        2.23 -     2.83: 4627
        2.83 -     3.42: 5735
        3.42 -     4.01: 6857
        4.01 -     4.60: 10408
  Nonbonded interactions: 27832
  Sorted by model distance:
  nonbonded model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" HB3 SER A  97 "
     model   vdw
     1.642 2.770
  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=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.738 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb="HD11 LEU A  93 "
            model="   0" pdb="HE21 GLN A 100 "
     model   vdw
     1.772 2.270
  ... (remaining 27827 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.617)
  Mean delta:    0.012 (Z=  0.645)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.149 (Z=  3.950)
  Mean delta:    1.606 (Z=  0.866)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -157.87   -22.13  5.00e+00  1.96e+01   4.4*sigma

  Min. delta:    0.019
  Max. delta:   87.347
  Mean delta:   12.084

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.214
  Mean delta:    0.077

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.079
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.459
    Angle     :  1.557   7.149   4079  Z= 0.666
    Chirality :  0.077   0.214    176
    Planarity :  0.008   0.060    327
    Dihedral  : 10.754  87.347    769
    Min Nonbonded Distance : 1.659
  
  Molprobity Statistics.
    All-atom Clashscore : 2.25
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  7.30 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  1.61 %
      Favored  : 97.58 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.04 (0.69), residues: 137
    helix:  0.88 (0.48), residues: 97
    sheet:  None (None), residues: 0
    loop :  0.52 (1.07), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.018   0.004   PHE A  67 
   TYR   0.074   0.009   TYR A  50 
   ARG   0.065   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.016   0.005   PHE A  67 
   TYR   0.061   0.011   TYR A  50 
   ARG   0.006   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 1
        1.22 -     1.42: 462
        1.42 -     1.61: 669
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.194  0.037 2.00e-02 2.50e+03 3.41e+00
  bond model="   0" pdb=" C   ASP A  74 "
       model="   0" pdb=" N   GLU A  75 "
    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   PRO A 117 "
       model="   0" pdb=" N   ASP A 118 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.57e+00
  bond model="   0" pdb=" C   TYR A 111 "
       model="   0" pdb=" N   VAL A 112 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.50e+00
  bond model="   0" pdb=" C   TYR A  81 "
       model="   0" pdb=" N   THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 1.96e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.39 -   106.49: 44
      106.49 -   112.59: 2740
      112.59 -   118.70: 417
      118.70 -   124.80: 833
      124.80 -   130.90: 45
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.96   -4.96 3.00e+00 1.11e-01 2.73e+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  113.40   -4.40 3.00e+00 1.11e-01 2.15e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.38   -4.38 3.00e+00 1.11e-01 2.13e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.25   -4.25 3.00e+00 1.11e-01 2.01e+00
  angle model="   0" pdb=" CA  HIS A 138 "
        model="   0" pdb=" CB  HIS A 138 "
        model="   0" pdb=" CG  HIS A 138 "
      ideal   model   delta    sigma   weight residual
     113.80  112.40    1.40 1.00e+00 1.00e+00 1.97e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 1006
       17.79 -    35.57: 10
       35.57 -    53.36: 11
       53.36 -    71.15: 4
       71.15 -    88.93: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CE1 TYR A  91 "
           model="   0" pdb=" CZ  TYR A  91 "
           model="   0" pdb=" OH  TYR A  91 "
           model="   0" pdb=" HH  TYR A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.93  -88.93     2      3.00e+01 1.11e-03 5.33e+00
  dihedral model="   0" pdb=" CB  GLN A  28 "
           model="   0" pdb=" CG  GLN A  28 "
           model="   0" pdb=" CD  GLN A  28 "
           model="   0" pdb=" OE1 GLN A  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   75.43  -75.43     2      3.00e+01 1.11e-03 5.00e+00
  dihedral model="   0" pdb=" CB  GLN A 100 "
           model="   0" pdb=" CG  GLN A 100 "
           model="   0" pdb=" CD  GLN A 100 "
           model="   0" pdb=" OE1 GLN A 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -70.47   70.47     2      3.00e+01 1.11e-03 4.74e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 106
       0.025 -    0.051: 49
       0.051 -    0.076: 6
       0.076 -    0.101: 10
       0.101 -    0.126: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.07e-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   -0.11 2.00e-01 2.50e+01 2.83e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.010 2.00e-02 2.50e+03   4.07e-03 4.96e-01
        model="   0" pdb=" CG  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.007 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 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.001 2.00e-02 2.50e+03   3.84e-03 4.42e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.002 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 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 "   -0.007 2.00e-02 2.50e+03   4.47e-03 3.99e-01
        model="   0" pdb=" CG  HIS A 139 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.24 -     1.91: 14
        1.91 -     2.58: 2306
        2.58 -     3.26: 6714
        3.26 -     3.93: 7868
        3.93 -     4.60: 12406
  Nonbonded interactions: 29308
  Sorted by model distance:
  nonbonded model="   0" pdb="HG12 ILE A  86 "
            model="   0" pdb=" HE1 TYR A  91 "
     model   vdw
     1.241 2.270
  nonbonded model="   0" pdb=" HB3 ASP A  47 "
            model="   0" pdb=" HD2 TYR A  50 "
     model   vdw
     1.651 2.270
  nonbonded model="   0" pdb=" O   LYS A  79 "
            model="   0" pdb=" HA2 GLY A  96 "
     model   vdw
     1.679 2.620
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.680 2.270
  nonbonded model="   0" pdb="HD12 ILE A  37 "
            model="   0" pdb="HD23 LEU A  61 "
     model   vdw
     1.719 2.440
  ... (remaining 29303 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   1.46 %
                favored =  91.24 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   2.25
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.56
  MolProbity score      =   1.51

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.032 (Z=  2.306)
  Mean delta:    0.004 (Z=  0.239)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.893 (Z=  1.506)
  Mean delta:    0.622 (Z=  0.299)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.020
  Max. delta:   80.937
  Mean delta:   12.532

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.161
  Mean delta:    0.038

                       ----------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   0.032   2242  Z= 0.170
    Angle     :  1.063   4.927   4079  Z= 0.378
    Chirality :  0.038   0.161    176
    Planarity :  0.002   0.021    327
    Dihedral  : 11.379  80.937    769
    Min Nonbonded Distance : 1.521
  
  Molprobity Statistics.
    All-atom Clashscore : 9.02
    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: -0.67 (0.66), residues: 137
    helix: -0.46 (0.54), residues: 76
    sheet:  None (None), residues: 0
    loop : -0.20 (0.77), residues: 61
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 136 
   PHE   0.005   0.002   PHE A  45 
   TYR   0.010   0.002   TYR A  12 
   ARG   0.005   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 136 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.009   0.002   TYR A 111 
   ARG   0.002   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   9.02
  RMS(bonds)            =   0.0028
  RMS(angles)           =   1.06
  MolProbity score      =   1.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  3.098)
  Mean delta:    0.012 (Z=  0.625)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.710 (Z=  3.923)
  Mean delta:    1.621 (Z=  0.897)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   152.90    27.10  5.00e+00  2.94e+01   5.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   155.02    24.98  5.00e+00  2.50e+01   5.0*sigma
   A  51  ILE  CA
   A  51  ILE  C
   A  52  PRO  N
   A  52  PRO  CA        180.00   156.13    23.87  5.00e+00  2.28e+01   4.8*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -158.11   -21.89  5.00e+00  1.92e+01   4.4*sigma

  Min. delta:    0.013
  Max. delta:   89.392
  Mean delta:   15.522

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.175
  Mean delta:    0.068

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.039
  Mean delta:    0.009

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.445
    Angle     :  1.558   6.710   4079  Z= 0.681
    Chirality :  0.068   0.175    176
    Planarity :  0.007   0.030    327
    Dihedral  : 13.245  89.392    769
    Min Nonbonded Distance : 1.393
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  6.57 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.81 %
      Favored  : 97.58 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.78 (0.70), residues: 137
    helix:  0.16 (0.53), residues: 68
    sheet:  None (None), residues: 0
    loop : -1.18 (0.83), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.024   0.005   PHE A  45 
   TYR   0.075   0.011   TYR A 111 
   ARG   0.033   0.006   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.014   0.005   PHE A  45 
   TYR   0.063   0.013   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN
   A 137  HIS

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  92.70 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.56
  MolProbity score      =   1.91

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: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.12 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 83
        1.23 -     1.43: 389
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.41e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.16e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 6.96e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.79e+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 6.73e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.17 -   106.00: 84
      106.00 -   111.84: 2506
      111.84 -   117.67: 487
      117.67 -   123.51: 861
      123.51 -   129.34: 141
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.69    3.91 1.00e+00 1.00e+00 1.53e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.36    4.84 1.30e+00 5.92e-01 1.39e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.05    3.55 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
        model="   0" pdb=" CD2 HIS A 137 "
      ideal   model   delta    sigma   weight residual
     131.20  126.59    4.61 1.30e+00 5.92e-01 1.26e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.12   -3.52 1.00e+00 1.00e+00 1.24e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.00: 961
       16.00 -    32.01: 49
       32.01 -    48.01: 16
       48.01 -    64.02: 4
       64.02 -    80.02: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.19   23.81     0      5.00e+00 4.00e-02 2.27e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.51   18.49     0      5.00e+00 4.00e-02 1.37e+01
  dihedral model="   0" pdb=" CA  SER A  98 "
           model="   0" pdb=" C   SER A  98 "
           model="   0" pdb=" N   LEU A  99 "
           model="   0" pdb=" CA  LEU A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.38   16.62     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.041: 77
       0.041 -    0.081: 39
       0.081 -    0.121: 39
       0.121 -    0.161: 18
       0.161 -    0.201: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.14e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.93e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.077 2.00e-02 2.50e+03   3.39e-02 3.46e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.070 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.025 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 "    0.020 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 "    0.013 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 "    0.012 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 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.030 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 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "    0.044 2.00e-02 2.50e+03   1.82e-02 9.90e+00
        model="   0" pdb=" CG  PHE A  15 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "    0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 123
        2.17 -     2.77: 4121
        2.77 -     3.38: 6147
        3.38 -     3.99: 7369
        3.99 -     4.60: 11150
  Nonbonded interactions: 28910
  Sorted by model distance:
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" HD1 TYR A  91 "
     model   vdw
     1.557 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.634 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.784 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.804 1.850
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" CD1 TYR A  91 "
     model   vdw
     1.817 2.970
  ... (remaining 28905 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: 4
        1.23 -     1.42: 461
        1.42 -     1.62: 667
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A  43 "
       model="   0" pdb=" N   ASP A  44 "
    ideal  model  delta    sigma   weight residual
    1.329  1.350 -0.021 1.40e-02 5.10e+03 2.19e+00
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.204  0.027 2.00e-02 2.50e+03 1.84e+00
  bond model="   0" pdb=" C   ALA A 115 "
       model="   0" pdb=" N   ASP A 116 "
    ideal  model  delta    sigma   weight residual
    1.329  1.348 -0.019 1.40e-02 5.10e+03 1.76e+00
  bond model="   0" pdb=" C   ASP A  47 "
       model="   0" pdb=" N   ALA A  48 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.48e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.48e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.82 -   106.92: 81
      106.92 -   113.01: 2687
      113.01 -   119.10: 442
      119.10 -   125.20: 827
      125.20 -   131.29: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.82    5.18 3.00e+00 1.11e-01 2.98e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  104.92    5.08 3.00e+00 1.11e-01 2.87e+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  114.02   -5.02 3.00e+00 1.11e-01 2.80e+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  113.92   -4.92 3.00e+00 1.11e-01 2.69e+00
  angle model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" CA  GLY A  80 "
        model="   0" pdb=" C   GLY A  80 "
      ideal   model   delta    sigma   weight residual
     113.30  118.04   -4.74 2.90e+00 1.19e-01 2.67e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 990
       17.73 -    35.47: 26
       35.47 -    53.20: 10
       53.20 -    70.94: 2
       70.94 -    88.67: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.67   88.67     1      3.00e+01 1.11e-03 1.04e+01
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.70   87.70     1      3.00e+01 1.11e-03 1.02e+01
  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  -79.80   79.80     1      3.00e+01 1.11e-03 8.78e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 111
       0.033 -    0.066: 47
       0.066 -    0.098: 13
       0.098 -    0.131: 1
       0.131 -    0.164: 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    2.60   -0.16 2.00e-01 2.50e+01 6.73e-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    2.58   -0.15 2.00e-01 2.50e+01 5.45e-01
  chirality model="   0" pdb=" CB  ILE A  86 "
            model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" CG1 ILE A  86 "
            model="   0" pdb=" CG2 ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.25e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "   -0.017 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  91 "   -0.010 2.00e-02 2.50e+03   5.93e-03 1.06e+00
        model="   0" pdb=" CG  TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.010 2.00e-02 2.50e+03   5.62e-03 9.46e-01
        model="   0" pdb=" CG  TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.012 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 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 51
        2.08 -     2.71: 3709
        2.71 -     3.34: 6108
        3.34 -     3.97: 7659
        3.97 -     4.60: 12001
  Nonbonded interactions: 29528
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LEU A  93 "
            model="   0" pdb="HD23 LEU A  99 "
     model   vdw
     1.451 2.620
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb="HG13 ILE A  86 "
     model   vdw
     1.506 2.270
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb="HG12 ILE A  86 "
     model   vdw
     1.577 2.270
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.718 1.850
  nonbonded model="   0" pdb=" HG  SER A  13 "
            model="   0" pdb=" OE1 GLN A  66 "
     model   vdw
     1.721 1.850
  ... (remaining 29523 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.27, 73.238, 46.684, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 93
        1.23 -     1.43: 379
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 9.16e+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 8.48e+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 8.03e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.25e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.48e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.96 -   105.76: 78
      105.76 -   111.56: 2428
      111.56 -   117.36: 551
      117.36 -   123.15: 816
      123.15 -   128.95: 206
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.64   -4.04 1.00e+00 1.00e+00 1.63e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.63    3.97 1.00e+00 1.00e+00 1.57e+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  126.19    5.01 1.30e+00 5.92e-01 1.48e+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  126.33    4.87 1.30e+00 5.92e-01 1.41e+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  126.48    4.72 1.30e+00 5.92e-01 1.32e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 964
       16.87 -    33.74: 45
       33.74 -    50.62: 17
       50.62 -    67.49: 6
       67.49 -    84.36: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.22   29.78     0      5.00e+00 4.00e-02 3.55e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.70   26.30     0      5.00e+00 4.00e-02 2.77e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.15   21.85     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 75
       0.041 -    0.081: 49
       0.081 -    0.122: 27
       0.122 -    0.162: 21
       0.162 -    0.203: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.18 2.00e-01 2.50e+01 8.44e-01
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.69   -0.18 2.00e-01 2.50e+01 8.16e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.077 2.00e-02 2.50e+03   3.32e-02 3.31e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 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 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.067 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.026 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 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.067 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.023 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.056 2.00e-02 2.50e+03   2.20e-02 1.45e+01
        model="   0" pdb=" CG  TYR A  89 "   -0.016 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 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 95
        2.14 -     2.76: 3953
        2.76 -     3.37: 6059
        3.37 -     3.99: 7128
        3.99 -     4.60: 10833
  Nonbonded interactions: 28068
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.530 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.706 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.743 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.780 1.850
  ... (remaining 28063 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.728)
  Mean delta:    0.012 (Z=  0.649)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.32     4.28  1.00e+00  1.83e+01   4.3*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.000 (Z=  4.282)
  Mean delta:    1.630 (Z=  0.885)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -153.70   -26.30  5.00e+00  2.77e+01   5.3*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   157.07    22.93  5.00e+00  2.10e+01   4.6*sigma

  Min. delta:    0.005
  Max. delta:   88.960
  Mean delta:   13.553

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.234
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.078
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  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   0.038   2242  Z= 0.462
    Angle     :  1.565   7.186   4079  Z= 0.675
    Chirality :  0.081   0.234    176
    Planarity :  0.009   0.074    327
    Dihedral  : 12.056  88.960    769
    Min Nonbonded Distance : 1.385
  
  Molprobity Statistics.
    All-atom Clashscore : 18.49
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  7.30 %
      Favored  : 92.70 %
    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: -0.05 (0.72), residues: 137
    helix:  0.39 (0.53), residues: 82
    sheet:  None (None), residues: 0
    loop : -0.54 (0.98), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.018   0.003   PHE A  45 
   TYR   0.165   0.016   TYR A  89 
   ARG   0.057   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.011   0.004   PHE A  45 
   TYR   0.133   0.019   TYR A  89 
   ARG   0.006   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.926)
  Mean delta:    0.012 (Z=  0.635)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        121.70   130.08    -8.38  1.80e+00  2.16e+01   4.7*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.375 (Z=  4.653)
  Mean delta:    1.682 (Z=  0.902)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00   154.57    25.43  5.00e+00  2.59e+01   5.1*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   157.80    22.20  5.00e+00  1.97e+01   4.4*sigma
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00  -159.66   -20.34  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.001
  Max. delta:   86.363
  Mean delta:   12.782

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.187
  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            0.054       0.093       58.89   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.054
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.452
    Angle     :  1.585   8.375   4079  Z= 0.684
    Chirality :  0.078   0.187    176
    Planarity :  0.008   0.053    327
    Dihedral  : 11.374  86.363    769
    Min Nonbonded Distance : 1.390
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  : 13.14 %
      Favored  : 84.67 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  1.61 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.86 (0.71), residues: 137
    helix: -0.87 (0.53), residues: 79
    sheet:  None (None), residues: 0
    loop : -1.63 (0.93), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 136 
   PHE   0.016   0.004   PHE A  45 
   TYR   0.114   0.014   TYR A  81 
   ARG   0.038   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 136 
   PHE   0.010   0.004   PHE A  67 
   TYR   0.093   0.016   TYR A  81 
   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 =  92.70 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =  18.49
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.57
  MolProbity score      =   2.52

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Ramachandran outliers =   2.19 %
                favored =  84.67 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.59
  MolProbity score      =   2.42

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.477)
  Mean delta:    0.012 (Z=  0.628)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.004 (Z=  0.002)
  Max. delta:    6.674 (Z=  4.100)
  Mean delta:    1.567 (Z=  0.852)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   156.51    23.49  5.00e+00  2.21e+01   4.7*sigma

  Min. delta:    0.078
  Max. delta:   89.433
  Mean delta:   12.691

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.200
  Mean delta:    0.076

                       ----------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   0.039   2242  Z= 0.447
    Angle     :  1.521   6.674   4079  Z= 0.654
    Chirality :  0.076   0.200    176
    Planarity :  0.009   0.049    327
    Dihedral  : 11.710  89.433    769
    Min Nonbonded Distance : 1.536
  
  Molprobity Statistics.
    All-atom Clashscore : 9.47
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.84 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  1.61 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.14 (0.69), residues: 137
    helix:  0.41 (0.50), residues: 89
    sheet:  None (None), residues: 0
    loop : -0.90 (0.96), residues: 48
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.106   0.015   PHE A  15 
   TYR   0.072   0.010   TYR A  50 
   ARG   0.048   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.068   0.016   PHE A  15 
   TYR   0.059   0.012   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  94.16 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   9.47
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.52
  MolProbity score      =   2.19

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.11 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 17
        1.23 -     1.42: 446
        1.42 -     1.62: 669
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.00e+00
  bond model="   0" pdb=" C   HIS A 136 "
       model="   0" pdb=" N   HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 1.99e+00
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+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  1.312  0.017 1.40e-02 5.10e+03 1.48e+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 1.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.53 -   106.60: 49
      106.60 -   112.68: 2712
      112.68 -   118.75: 441
      118.75 -   124.82: 833
      124.82 -   130.90: 44
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.67   -4.67 3.00e+00 1.11e-01 2.43e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.49   -4.49 3.00e+00 1.11e-01 2.24e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.45   -4.45 3.00e+00 1.11e-01 2.20e+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  113.43   -4.43 3.00e+00 1.11e-01 2.19e+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  104.58    4.42 3.00e+00 1.11e-01 2.17e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 984
       17.90 -    35.80: 21
       35.80 -    53.71: 12
       53.71 -    71.61: 7
       71.61 -    89.51: 9
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A  44 "
           model="   0" pdb=" CB  ASP A  44 "
           model="   0" pdb=" CG  ASP A  44 "
           model="   0" pdb=" OD1 ASP A  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.34   58.34     1      2.00e+01 2.50e-03 1.14e+01
  dihedral model="   0" pdb=" CA  ASP A  88 "
           model="   0" pdb=" CB  ASP A  88 "
           model="   0" pdb=" CG  ASP A  88 "
           model="   0" pdb=" OD1 ASP A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.66   57.66     1      2.00e+01 2.50e-03 1.12e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.51   89.51     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 111
       0.029 -    0.058: 48
       0.058 -    0.087: 4
       0.087 -    0.116: 8
       0.116 -    0.145: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.78e-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    2.57   -0.13 2.00e-01 2.50e+01 4.33e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.014 2.00e-02 2.50e+03   5.22e-03 8.18e-01
        model="   0" pdb=" CG  TYR A 111 "    0.007 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 "    0.001 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 "    0.003 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 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.012 2.00e-02 2.50e+03   5.12e-03 7.87e-01
        model="   0" pdb=" CG  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.000 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 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.001 2.00e-02 2.50e+03   4.55e-03 6.20e-01
        model="   0" pdb=" CG  TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.24: 268
        2.24 -     2.83: 4997
        2.83 -     3.42: 5748
        3.42 -     4.01: 7619
        4.01 -     4.60: 11271
  Nonbonded interactions: 29903
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.656 1.850
  nonbonded model="   0" pdb=" OD1 ASP A 118 "
            model="   0" pdb=" HZ1 LYS A 125 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.736 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.740 2.270
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.771 1.850
  ... (remaining 29898 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.956)
  Mean delta:    0.012 (Z=  0.643)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    9.476 (Z=  4.191)
  Mean delta:    1.671 (Z=  0.885)

                      ----------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   141.99    38.01  5.00e+00  5.78e+01   7.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   144.39    35.61  5.00e+00  5.07e+01   7.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   145.11    34.89  5.00e+00  4.87e+01   7.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   145.47    34.53  5.00e+00  4.77e+01   6.9*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -150.67   -29.33  5.00e+00  3.44e+01   5.9*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   151.88    28.12  5.00e+00  3.16e+01   5.6*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   152.95    27.05  5.00e+00  2.93e+01   5.4*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   154.51    25.49  5.00e+00  2.60e+01   5.1*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   156.10    23.90  5.00e+00  2.28e+01   4.8*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   156.30    23.70  5.00e+00  2.25e+01   4.7*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   156.80    23.20  5.00e+00  2.15e+01   4.6*sigma

  Min. delta:    0.006
  Max. delta:   83.312
  Mean delta:   12.913

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.244
  Mean delta:    0.079

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.043
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.458
    Angle     :  1.596   9.476   4079  Z= 0.680
    Chirality :  0.079   0.244    176
    Planarity :  0.007   0.043    327
    Dihedral  : 11.807  83.312    769
    Min Nonbonded Distance : 1.753
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  : 10.22 %
      Favored  : 85.40 %
    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 : 3.05 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.07 (0.71), residues: 137
    helix: -0.66 (0.53), residues: 76
    sheet:  None (None), residues: 0
    loop : -0.58 (0.92), residues: 61
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.064   0.008   TYR A  50 
   ARG   0.037   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.054   0.010   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   4.38 %
                favored =  85.40 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.60
  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      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  3.013)
  Mean delta:    0.012 (Z=  0.634)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.986 (Z=  3.749)
  Mean delta:    1.591 (Z=  0.868)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   151.70    28.30  5.00e+00  3.20e+01   5.7*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   153.46    26.54  5.00e+00  2.82e+01   5.3*sigma

  Min. delta:    0.027
  Max. delta:   89.236
  Mean delta:   12.009

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.210
  Mean delta:    0.072

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.056
  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   2242  Z= 0.452
    Angle     :  1.535   6.986   4079  Z= 0.664
    Chirality :  0.072   0.210    176
    Planarity :  0.008   0.042    327
    Dihedral  : 11.193  89.236    769
    Min Nonbonded Distance : 1.352
  
  Molprobity Statistics.
    All-atom Clashscore : 21.19
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  5.11 %
      Favored  : 91.97 %
    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: -0.32 (0.67), residues: 137
    helix:  0.28 (0.52), residues: 85
    sheet:  None (None), residues: 0
    loop : -0.89 (0.85), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.084   0.013   PHE A  15 
   TYR   0.048   0.008   TYR A  91 
   ARG   0.044   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A  43 
   PHE   0.054   0.014   PHE A  15 
   TYR   0.039   0.010   TYR A  91 
   ARG   0.006   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   2.92 %
                favored =  91.97 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  21.19
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.54
  MolProbity score      =   2.47

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.021 (Z=  1.475)
  Mean delta:    0.004 (Z=  0.260)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.452 (Z=  1.484)
  Mean delta:    0.555 (Z=  0.281)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.004
  Max. delta:   65.174
  Mean delta:    9.874

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.142
  Mean delta:    0.037

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.017
  Mean delta:    0.002

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.021   2242  Z= 0.186
    Angle     :  1.033   5.001   4079  Z= 0.368
    Chirality :  0.037   0.142    176
    Planarity :  0.002   0.017    327
    Dihedral  :  9.381  81.273    769
    Min Nonbonded Distance : 1.679
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.19 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.81 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.91 (0.66), residues: 137
    helix: -1.33 (0.52), residues: 80
    sheet:  None (None), residues: 0
    loop : -0.94 (0.81), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.006   0.002   PHE A  15 
   TYR   0.009   0.002   TYR A  12 
   ARG   0.004   0.001   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.003   0.001   PHE A  15 
   TYR   0.006   0.002   TYR A  12 
   ARG   0.002   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 135  HIS
   A 137  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.431)
  Mean delta:    0.012 (Z=  0.635)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.228 (Z=  3.992)
  Mean delta:    1.628 (Z=  0.883)

                      ----------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   154.51    25.49  5.00e+00  2.60e+01   5.1*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   156.50    23.50  5.00e+00  2.21e+01   4.7*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -157.11   -22.89  5.00e+00  2.10e+01   4.6*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   157.19    22.81  5.00e+00  2.08e+01   4.6*sigma
   A 127  ARG  CA
   A 127  ARG  C
   A 128  MET  N
   A 128  MET  CA        180.00   158.81    21.19  5.00e+00  1.80e+01   4.2*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   159.33    20.67  5.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.054
  Max. delta:   85.233
  Mean delta:   11.831

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.188
  Mean delta:    0.077

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.042
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.452
    Angle     :  1.557   6.228   4079  Z= 0.673
    Chirality :  0.077   0.188    176
    Planarity :  0.008   0.042    327
    Dihedral  : 11.862  89.944    769
    Min Nonbonded Distance : 1.350
  
  Molprobity Statistics.
    All-atom Clashscore : 7.21
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  : 10.95 %
      Favored  : 85.40 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  1.61 %
      Favored  : 97.58 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.78 (0.69), residues: 137
    helix: -0.53 (0.53), residues: 72
    sheet:  None (None), residues: 0
    loop : -1.92 (0.83), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.020   0.004   PHE A  45 
   TYR   0.061   0.011   TYR A  50 
   ARG   0.033   0.007   ARG A  58 

  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  45 
   TYR   0.051   0.014   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.045 (Z=  2.938)
  Mean delta:    0.012 (Z=  0.635)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.105 (Z=  4.089)
  Mean delta:    1.564 (Z=  0.861)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.010
  Max. delta:   89.869
  Mean delta:   12.767

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.251
  Mean delta:    0.076

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.042
  Mean delta:    0.010

============================= 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   0.045   2242  Z= 0.452
    Angle     :  1.522   7.105   4079  Z= 0.659
    Chirality :  0.076   0.251    176
    Planarity :  0.007   0.032    327
    Dihedral  : 11.734  89.869    769
    Min Nonbonded Distance : 1.487
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  0.73 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  3.23 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.32 (0.67), residues: 137
    helix:  0.45 (0.53), residues: 83
    sheet:  None (None), residues: 0
    loop :  0.05 (0.82), residues: 54
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.017   0.005   PHE A  15 
   TYR   0.068   0.009   TYR A  50 
   ARG   0.036   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.011   0.005   PHE A  67 
   TYR   0.056   0.011   TYR A  50 
   ARG   0.003   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Ramachandran outliers =   1.46 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.03
  MolProbity score      =   1.69

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   3.65 %
                favored =  85.40 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   7.21
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.56
  MolProbity score      =   2.05

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  98.54 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.52
  MolProbity score      =   1.48

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.027 (Z=  1.346)
  Mean delta:    0.004 (Z=  0.253)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    5.075 (Z=  1.692)
  Mean delta:    0.589 (Z=  0.299)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   86.372
  Mean delta:   14.057

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.142
  Mean delta:    0.041

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.017
  Mean delta:    0.002

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 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   0.027   2242  Z= 0.181
    Angle     :  1.056   5.075   4079  Z= 0.378
    Chirality :  0.041   0.142    176
    Planarity :  0.002   0.017    327
    Dihedral  : 12.137  86.372    769
    Min Nonbonded Distance : 1.252
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  4.03 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  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: -0.27 (0.72), residues: 137
    helix: -0.05 (0.63), residues: 63
    sheet:  None (None), residues: 0
    loop : -0.17 (0.78), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.004   0.001   PHE A  45 
   TYR   0.014   0.003   TYR A  89 
   ARG   0.004   0.001   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.010   0.003   TYR A  12 
   ARG   0.001   0.000   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A GLU   75": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  2.755)
  Mean delta:    0.012 (Z=  0.630)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.498 (Z=  3.683)
  Mean delta:    1.576 (Z=  0.861)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   157.52    22.48  5.00e+00  2.02e+01   4.5*sigma

  Min. delta:    0.117
  Max. delta:   80.028
  Mean delta:   12.521

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.219
  Mean delta:    0.079

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  36  ASP  CB
   A  36  ASP  CG
   A  36  ASP  OD1
   A  36  ASP  OD2           0.047       0.081       22.02   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.041   2242  Z= 0.449
    Angle     :  1.529   6.498   4079  Z= 0.660
    Chirality :  0.079   0.219    176
    Planarity :  0.008   0.047    327
    Dihedral  : 11.127  80.028    769
    Min Nonbonded Distance : 1.482
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  1.61 %
      Favored  : 97.58 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  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: -0.38 (0.70), residues: 137
    helix:  0.11 (0.54), residues: 79
    sheet:  None (None), residues: 0
    loop : -0.62 (0.89), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.015   0.005   PHE A  45 
   TYR   0.068   0.012   TYR A  50 
   ARG   0.039   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.005   PHE A  67 
   TYR   0.056   0.014   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0031
  RMS(angles)           =   1.06
  MolProbity score      =   1.77

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  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.53
  MolProbity score      =   1.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.708)
  Mean delta:    0.012 (Z=  0.610)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.204 (Z=  3.497)
  Mean delta:    1.558 (Z=  0.843)

                      ----------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   159.84    20.16  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.018
  Max. delta:   87.536
  Mean delta:   13.158

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.174
  Mean delta:    0.072

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.434
    Angle     :  1.515   6.204   4079  Z= 0.649
    Chirality :  0.072   0.174    176
    Planarity :  0.008   0.047    327
    Dihedral  : 11.223  87.536    769
    Min Nonbonded Distance : 1.451
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  6.57 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  1.61 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.53 (0.69), residues: 137
    helix: -0.20 (0.48), residues: 90
    sheet:  None (None), residues: 0
    loop : -0.35 (1.02), residues: 47
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.013   0.003   PHE A  45 
   TYR   0.063   0.010   TYR A  50 
   ARG   0.031   0.008   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   0.052   0.012   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  92.70 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.52
  MolProbity score      =   2.44

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.037 (Z=  1.847)
  Mean delta:    0.005 (Z=  0.289)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.956 (Z=  1.652)
  Mean delta:    0.608 (Z=  0.320)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   75.428
  Mean delta:    9.254

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.126
  Mean delta:    0.037

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.015
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.037   2242  Z= 0.206
    Angle     :  1.033   4.956   4079  Z= 0.376
    Chirality :  0.037   0.126    176
    Planarity :  0.002   0.015    327
    Dihedral  :  9.437  88.935    769
    Min Nonbonded Distance : 1.241
  
  Molprobity Statistics.
    All-atom Clashscore : 11.72
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.14 (0.65), residues: 137
    helix: -0.23 (0.55), residues: 70
    sheet:  None (None), residues: 0
    loop :  0.28 (0.71), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.005   0.002   PHE A  67 
   TYR   0.010   0.002   TYR A  12 
   ARG   0.006   0.002   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.007   0.002   TYR A  12 
   ARG   0.004   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.772)
  Mean delta:    0.011 (Z=  0.603)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:    6.622 (Z=  4.030)
  Mean delta:    1.568 (Z=  0.862)

                      ----------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   156.73    23.27  5.00e+00  2.17e+01   4.7*sigma

  Min. delta:    0.000
  Max. delta:   81.459
  Mean delta:   13.997

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.200
  Mean delta:    0.076

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.067
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.430
    Angle     :  1.526   6.622   4079  Z= 0.660
    Chirality :  0.076   0.200    176
    Planarity :  0.009   0.064    327
    Dihedral  : 12.236  81.459    769
    Min Nonbonded Distance : 1.537
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  2.42 %
      Favored  : 91.94 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.22 (0.70), residues: 137
    helix: -0.17 (0.51), residues: 84
    sheet:  None (None), residues: 0
    loop :  0.20 (0.97), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.012   0.003   PHE A  45 
   TYR   0.149   0.017   TYR A  81 
   ARG   0.042   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.011   0.003   PHE A  67 
   TYR   0.120   0.020   TYR A  81 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  11.72
  RMS(bonds)            =   0.0033
  RMS(angles)           =   1.03
  MolProbity score      =   1.75

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  1.363)
  Mean delta:    0.004 (Z=  0.231)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.030 (Z=  1.515)
  Mean delta:    0.690 (Z=  0.315)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   82.428
  Mean delta:   11.212

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.152
  Mean delta:    0.045

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.023
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.021   2242  Z= 0.165
    Angle     :  1.079   4.957   4079  Z= 0.383
    Chirality :  0.045   0.152    176
    Planarity :  0.002   0.023    327
    Dihedral  : 10.717  82.428    769
    Min Nonbonded Distance : 1.658
  
  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:  0.61 (0.69), residues: 137
    helix: -0.13 (0.63), residues: 68
    sheet:  2.18 (1.77), residues: 10
    loop :  1.05 (0.72), residues: 59
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.005   0.001   PHE A  45 
   TYR   0.011   0.003   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.010   0.003   TYR A 111 
   ARG   0.002   0.000   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.023 (Z=  2.112)
  Mean delta:    0.008 (Z=  0.424)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.925 (Z=  3.847)
  Mean delta:    1.090 (Z=  0.572)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.024
  Max. delta:   88.306
  Mean delta:   11.134

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.254
  Mean delta:    0.055

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.027
  Mean delta:    0.006

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 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      :  0.006   0.023   2242  Z= 0.302
    Angle     :  1.277   6.925   4079  Z= 0.505
    Chirality :  0.055   0.254    176
    Planarity :  0.004   0.020    327
    Dihedral  : 10.261  88.306    769
    Min Nonbonded Distance : 1.579
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 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:  0.41 (0.69), residues: 137
    helix:  0.29 (0.50), residues: 91
    sheet:  None (None), residues: 0
    loop :  0.60 (1.00), residues: 46
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.001   HIS A 139 
   PHE   0.007   0.002   PHE A  15 
   TYR   0.036   0.006   TYR A  12 
   ARG   0.022   0.005   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.001   HIS A 139 
   PHE   0.003   0.002   PHE A  67 
   TYR   0.030   0.007   TYR A  12 
   ARG   0.002   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.53
  MolProbity score      =   2.44

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.66
  RMS(bonds)            =   0.0057
  RMS(angles)           =   1.28
  MolProbity score      =   1.58

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            =   4.51
  RMS(bonds)            =   0.0027
  RMS(angles)           =   1.08
  MolProbity score      =   1.23

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.73, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (70.825, 43.505, 44.528, 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     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.927)
  Mean delta:    0.011 (Z=  0.563)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.796 (Z=  3.438)
  Mean delta:    1.448 (Z=  0.798)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -156.13   -23.87  5.00e+00  2.28e+01   4.8*sigma

  Min. delta:    0.010
  Max. delta:   86.386
  Mean delta:   12.308

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.173
  Mean delta:    0.067

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.045
  Mean delta:    0.009

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.401
    Angle     :  1.445   6.796   4079  Z= 0.620
    Chirality :  0.067   0.173    176
    Planarity :  0.007   0.034    327
    Dihedral  : 11.218  87.993    769
    Min Nonbonded Distance : 1.769
  
  Molprobity Statistics.
    All-atom Clashscore : 1.80
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.81 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.20 (0.67), residues: 137
    helix: -0.23 (0.55), residues: 71
    sheet:  None (None), residues: 0
    loop :  0.81 (0.78), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 137 
   PHE   0.021   0.005   PHE A  45 
   TYR   0.059   0.008   TYR A  12 
   ARG   0.036   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 137 
   PHE   0.014   0.005   PHE A  67 
   TYR   0.048   0.009   TYR A  12 
   ARG   0.005   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   1.80
  RMS(bonds)            =   0.0077
  RMS(angles)           =   1.45
  MolProbity score      =   1.24

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.477)
  Mean delta:    0.012 (Z=  0.628)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.004 (Z=  0.002)
  Max. delta:    6.674 (Z=  4.100)
  Mean delta:    1.567 (Z=  0.852)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   156.51    23.49  5.00e+00  2.21e+01   4.7*sigma

  Min. delta:    0.078
  Max. delta:   89.433
  Mean delta:   12.691

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.200
  Mean delta:    0.076

                       ----------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   0.039   2242  Z= 0.447
    Angle     :  1.521   6.674   4079  Z= 0.654
    Chirality :  0.076   0.200    176
    Planarity :  0.009   0.049    327
    Dihedral  : 11.710  89.433    769
    Min Nonbonded Distance : 1.536
  
  Molprobity Statistics.
    All-atom Clashscore : 9.47
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.84 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  1.61 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.14 (0.69), residues: 137
    helix:  0.41 (0.50), residues: 89
    sheet:  None (None), residues: 0
    loop : -0.90 (0.96), residues: 48
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.106   0.015   PHE A  15 
   TYR   0.072   0.010   TYR A  50 
   ARG   0.048   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.068   0.016   PHE A  15 
   TYR   0.059   0.012   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  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: 0.77, per 1000 atoms: 0.35
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.461, 62.592, 57.417, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

  Ramachandran outliers =   0.00 %
                favored =  94.16 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   9.47
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.52
  MolProbity score      =   2.19

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.042 (Z=  3.019)
  Mean delta:    0.012 (Z=  0.665)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.725 (Z=  3.956)
  Mean delta:    1.658 (Z=  0.895)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.025
  Max. delta:   89.030
  Mean delta:   12.794

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.263
  Mean delta:    0.085

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.052
  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   0.042   2242  Z= 0.473
    Angle     :  1.591  10.925   4079  Z= 0.685
    Chirality :  0.085   0.263    176
    Planarity :  0.008   0.052    327
    Dihedral  : 12.096  89.030    769
    Min Nonbonded Distance : 1.359
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    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 : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.21 (0.66), residues: 137
    helix: -0.82 (0.48), residues: 86
    sheet:  None (None), residues: 0
    loop : -0.44 (0.89), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.013   0.003   PHE A  67 
   TYR   0.066   0.009   TYR A  50 
   ARG   0.038   0.008   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.013   0.003   PHE A  67 
   TYR   0.054   0.011   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   7.66
  RMS(bonds)            =   0.0088
  RMS(angles)           =   1.59
  MolProbity score      =   1.87

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.131)
  Mean delta:    0.012 (Z=  0.649)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.039 (Z=  3.866)
  Mean delta:    1.607 (Z=  0.870)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   141.73    38.27  5.00e+00  5.86e+01   7.7*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   157.55    22.45  5.00e+00  2.02e+01   4.5*sigma

  Min. delta:    0.014
  Max. delta:   89.242
  Mean delta:   13.312

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.224
  Mean delta:    0.081

                       ----------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   0.040   2242  Z= 0.462
    Angle     :  1.546   8.039   4079  Z= 0.666
    Chirality :  0.081   0.224    176
    Planarity :  0.008   0.038    327
    Dihedral  : 12.174  89.242    769
    Min Nonbonded Distance : 1.568
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    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 : 0.76 %
  
  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: -0.58 (0.70), residues: 137
    helix: -0.31 (0.51), residues: 85
    sheet:  None (None), residues: 0
    loop : -0.25 (0.97), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.060   0.008   TYR A 111 
   ARG   0.036   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.051   0.010   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.772)
  Mean delta:    0.011 (Z=  0.603)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.005 (Z=  0.002)
  Max. delta:    6.622 (Z=  4.030)
  Mean delta:    1.568 (Z=  0.862)

                      ----------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   156.73    23.27  5.00e+00  2.17e+01   4.7*sigma

  Min. delta:    0.000
  Max. delta:   81.459
  Mean delta:   13.997

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.200
  Mean delta:    0.076

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.067
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.430
    Angle     :  1.526   6.622   4079  Z= 0.660
    Chirality :  0.076   0.200    176
    Planarity :  0.009   0.064    327
    Dihedral  : 12.236  81.459    769
    Min Nonbonded Distance : 1.537
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  2.42 %
      Favored  : 91.94 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.22 (0.70), residues: 137
    helix: -0.17 (0.51), residues: 84
    sheet:  None (None), residues: 0
    loop :  0.20 (0.97), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.012   0.003   PHE A  45 
   TYR   0.149   0.017   TYR A  81 
   ARG   0.042   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.011   0.003   PHE A  67 
   TYR   0.120   0.020   TYR A  81 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (52.857, 65.476, 60.445, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   0.73 %
                favored =  94.16 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.55
  MolProbity score      =   2.11

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.53
  MolProbity score      =   2.44

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: (37.632, 69.64, 77.114, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.701)
  Mean delta:    0.012 (Z=  0.623)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.108 (Z=  4.134)
  Mean delta:    1.647 (Z=  0.887)

                      ----------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   152.59    27.41  5.00e+00  3.00e+01   5.5*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -154.13   -25.87  5.00e+00  2.68e+01   5.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   154.47    25.53  5.00e+00  2.61e+01   5.1*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   157.11    22.89  5.00e+00  2.10e+01   4.6*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   158.99    21.01  5.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.012
  Max. delta:   87.838
  Mean delta:   13.586

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.273
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.058
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.444
    Angle     :  1.570   8.108   4079  Z= 0.676
    Chirality :  0.080   0.273    176
    Planarity :  0.008   0.043    327
    Dihedral  : 11.862  87.838    769
    Min Nonbonded Distance : 1.556
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  7.30 %
      Favored  : 90.51 %
    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: -0.82 (0.69), residues: 137
    helix: -0.08 (0.50), residues: 93
    sheet:  None (None), residues: 0
    loop : -1.35 (0.99), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.069   0.009   TYR A  50 
   ARG   0.047   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.057   0.012   TYR A  50 
   ARG   0.006   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.01 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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.

  Ramachandran outliers =   2.19 %
                favored =  90.51 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.57
  MolProbity score      =   2.07

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 7
        1.23 -     1.42: 458
        1.42 -     1.61: 667
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.390 -0.016 1.10e-02 8.26e+03 2.06e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.51e+00
  bond model="   0" pdb=" C   PRO A 114 "
       model="   0" pdb=" N   ALA A 115 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.49e+00
  bond model="   0" pdb=" C   HIS A 136 "
       model="   0" pdb=" N   HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.28e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.332 -0.011 1.00e-02 1.00e+04 1.21e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.55 -   106.63: 52
      106.63 -   112.70: 2722
      112.70 -   118.78: 431
      118.78 -   124.85: 832
      124.85 -   130.93: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.84   -4.84 3.00e+00 1.11e-01 2.60e+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  113.74   -4.74 3.00e+00 1.11e-01 2.49e+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  113.49   -4.49 3.00e+00 1.11e-01 2.24e+00
  angle model="   0" pdb=" NE  ARG A 129 "
        model="   0" pdb=" CZ  ARG A 129 "
        model="   0" pdb=" NH1 ARG A 129 "
      ideal   model   delta    sigma   weight residual
     121.50  120.01    1.49 1.00e+00 1.00e+00 2.23e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.40   -4.40 3.00e+00 1.11e-01 2.15e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 986
       16.65 -    33.30: 23
       33.30 -    49.95: 10
       49.95 -    66.60: 10
       66.60 -    83.25: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  75 "
           model="   0" pdb=" CG  GLU A  75 "
           model="   0" pdb=" CD  GLU A  75 "
           model="   0" pdb=" OE1 GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   83.25  -83.25     1      3.00e+01 1.11e-03 9.41e+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   78.62  -78.62     1      3.00e+01 1.11e-03 8.56e+00
  dihedral model="   0" pdb=" CA  ASP A  47 "
           model="   0" pdb=" CB  ASP A  47 "
           model="   0" pdb=" CG  ASP A  47 "
           model="   0" pdb=" OD1 ASP A  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -71.05   41.05     1      2.00e+01 2.50e-03 5.90e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 120
       0.030 -    0.059: 39
       0.059 -    0.089: 3
       0.089 -    0.118: 10
       0.118 -    0.148: 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    2.58   -0.15 2.00e-01 2.50e+01 5.47e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.06e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.015 2.00e-02 2.50e+03   5.90e-03 1.04e+00
        model="   0" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.002 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=" C   THR A   5 "    0.013 5.00e-02 4.00e+02   2.05e-02 6.73e-01
        model="   0" pdb=" N   PRO A   6 "   -0.035 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 "    0.011 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  68 "    0.008 2.00e-02 2.50e+03   3.80e-03 4.34e-01
        model="   0" pdb=" CG  TYR A  68 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  68 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  68 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  68 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  68 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  68 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  68 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  68 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  68 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  68 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.03: 34
        2.03 -     2.67: 3215
        2.67 -     3.32: 6404
        3.32 -     3.96: 7860
        3.96 -     4.60: 11953
  Nonbonded interactions: 29466
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 TYR A  81 "
            model="   0" pdb="HD11 ILE A  86 "
     model   vdw
     1.389 2.440
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" OH  TYR A  89 "
     model   vdw
     1.541 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.603 1.850
  nonbonded model="   0" pdb=" HE2 TYR A  91 "
            model="   0" pdb="HD11 LEU A  93 "
     model   vdw
     1.681 2.270
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" O   ASP A  44 "
     model   vdw
     1.753 2.620
  ... (remaining 29461 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: 108
        1.23 -     1.43: 364
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.11e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.08e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.61e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.44e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.88e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.08 -   105.05: 46
      105.05 -   111.03: 2328
      111.03 -   117.01: 668
      117.01 -   122.99: 802
      122.99 -   128.97: 235
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   THR A  82 "
        model="   0" pdb=" CA  THR A  82 "
        model="   0" pdb=" CB  THR A  82 "
      ideal   model   delta    sigma   weight residual
     111.50  118.22   -6.72 1.70e+00 3.46e-01 1.56e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.68    3.92 1.00e+00 1.00e+00 1.53e+01
  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   99.08   10.92 3.00e+00 1.11e-01 1.33e+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  126.52    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  119.23    3.37 1.00e+00 1.00e+00 1.13e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 963
       17.81 -    35.61: 45
       35.61 -    53.42: 19
       53.42 -    71.22: 5
       71.22 -    89.03: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.48   19.52     0      5.00e+00 4.00e-02 1.52e+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  161.30   18.70     0      5.00e+00 4.00e-02 1.40e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.18   16.82     0      5.00e+00 4.00e-02 1.13e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 76
       0.053 -    0.105: 61
       0.105 -    0.158: 31
       0.158 -    0.211: 6
     
============================== Collecting inputs ==============================

  0.211 -    0.263: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CB  THR A  82 "
            model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" OG1 THR A  82 "
            model="   0" pdb=" CG2 THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.066 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 "   -0.015 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 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.058 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 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.014 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   2.22e-02 1.48e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 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 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.005 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 9.42e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.003 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 "    0.028 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
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.36 -     2.01: 30
        2.01 -     2.66: 290
  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
8
        2.66 -     3.30: 6446
        3.30 -     3.95: 7672
        3.95 -     4.60: 11555
  Nonbonded interactions: 28611
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb="HG13 ILE A  77 "
     model   vdw
     1.359 2.620
  nonbonded model="   0" pdb=" HG  SER A  17 "
            model="   0" pdb=" OE2 GLU A  84 "
     model   vdw
     1.525 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.636 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.683 1.850
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" OE1 GLU A  84 "
     model   vdw
     1.750 2.450
  ... (remaining 28606 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.979)
  Mean delta:    0.012 (Z=  0.634)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.36     4.24  1.00e+00  1.80e+01   4.2*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    6.198 (Z=  4.241)
  Mean delta:    1.585 (Z=  0.858)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   152.29    27.71  5.00e+00  3.07e+01   5.5*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   152.74    27.26  5.00e+00  2.97e+01   5.5*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   154.81    25.19  5.00e+00  2.54e+01   5.0*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   157.89    22.11  5.00e+00  1.96e+01   4.4*sigma

  Min. delta:    0.053
  Max. delta:   88.994
  Mean delta:   11.461

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.192
  Mean delta:    0.073

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  36  ASP  CB
   A  36  ASP  CG
   A  36  ASP  OD1
   A  36  ASP  OD2           0.051       0.088       25.71   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.051
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.451
    Angle     :  1.531   6.198   4079  Z= 0.658
    Chirality :  0.073   0.192    176
    Planarity :  0.008   0.051    327
    Dihedral  : 10.526  88.994    769
    Min Nonbonded Distance : 1.514
  
  Molprobity Statistics.
    All-atom Clashscore : 7.21
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.31 (0.70), residues: 137
    helix:  0.21 (0.55), residues: 72
    sheet:  None (None), residues: 0
    loop :  0.43 (0.84), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.060   0.009   TYR A 111 
   ARG   0.035   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.051   0.010   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 =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.21
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.53
  MolProbity score      =   1.70

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.024 (Z=  1.386)
  Mean delta:    0.004 (Z=  0.249)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.636 (Z=  1.481)
  Mean delta:    0.682 (Z=  0.337)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   74.579
  Mean delta:    7.656

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.144
  Mean delta:    0.036

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.021
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.024   2242  Z= 0.177
    Angle     :  1.057   5.020   4079  Z= 0.384
    Chirality :  0.036   0.144    176
    Planarity :  0.002   0.021    327
    Dihedral  :  7.999  79.305    769
    Min Nonbonded Distance : 1.609
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.72 (0.63), residues: 137
    helix: -0.28 (0.56), residues: 72
    sheet:  None (None), residues: 0
    loop : -0.55 (0.67), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.007   0.002   PHE A  45 
   TYR   0.007   0.002   TYR A  91 
   ARG   0.005   0.001   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.006   0.001   TYR A 111 
   ARG   0.003   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.662)
  Mean delta:    0.012 (Z=  0.610)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.505 (Z=  3.989)
  Mean delta:    1.631 (Z=  0.879)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 123  GLU  CA
   A 123  GLU  C
   A 124  ALA  N
   A 124  ALA  CA        180.00   148.80    31.20  5.00e+00  3.89e+01   6.2*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   155.06    24.94  5.00e+00  2.49e+01   5.0*sigma
   A 122  ILE  CA
   A 122  ILE  C
   A 123  GLU  N
   A 123  GLU  CA        180.00   155.64    24.36  5.00e+00  2.37e+01   4.9*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   157.77    22.23  5.00e+00  1.98e+01   4.4*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   158.11    21.89  5.00e+00  1.92e+01   4.4*sigma
   A 120  GLU  CA
   A 120  GLU  C
   A 121  GLY  N
   A 121  GLY  CA        180.00  -158.49   -21.51  5.00e+00  1.85e+01   4.3*sigma

  Min. delta:    0.041
  Max. delta:   87.872
  Mean delta:   12.770

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.246
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.043
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.434
    Angle     :  1.566   7.146   4079  Z= 0.673
    Chirality :  0.080   0.246    176
    Planarity :  0.008   0.042    327
    Dihedral  : 12.039  87.872    769
    Min Nonbonded Distance : 1.589
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  8.03 %
      Favored  : 89.05 %
    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 : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.84 (0.67), residues: 137
    helix: -0.64 (0.55), residues: 75
    sheet:  None (None), residues: 0
    loop : -1.91 (0.78), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 134 
   PHE   0.015   0.004   PHE A  67 
   TYR   0.073   0.010   TYR A  50 
   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 134 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.061   0.012   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0029
  RMS(angles)           =   1.06
  MolProbity score      =   1.26

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   2.92 %
                favored =  89.05 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.57
  MolProbity score      =   2.02

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.772, 73.06, 73.858, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  1.543)
  Mean delta:    0.004 (Z=  0.268)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.053 (Z=  1.615)
  Mean delta:    0.649 (Z=  0.308)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   85.590
  Mean delta:   14.507

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.167
  Mean delta:    0.048

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.022
  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   2242  Z= 0.191
    Angle     :  1.077   4.860   4079  Z= 0.384
    Chirality :  0.048   0.167    176
    Planarity :  0.002   0.022    327
    Dihedral  : 12.619  85.590    769
    Min Nonbonded Distance : 1.474
  
  Molprobity Statistics.
    All-atom Clashscore : 9.02
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.40 (0.71), residues: 137
    helix: -0.27 (0.60), residues: 63
    sheet:  None (None), residues: 0
    loop :  1.01 (0.78), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.006   0.002   PHE A  67 
   TYR   0.018   0.003   TYR A  50 
   ARG   0.005   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.004   0.002   PHE A  67 
   TYR   0.015   0.004   TYR A  50 
   ARG   0.002   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 136  HIS

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  2.755)
  Mean delta:    0.012 (Z=  0.630)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.498 (Z=  3.683)
  Mean delta:    1.576 (Z=  0.861)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   157.52    22.48  5.00e+00  2.02e+01   4.5*sigma

  Min. delta:    0.117
  Max. delta:   80.028
  Mean delta:   12.521

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.219
  Mean delta:    0.079

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  36  ASP  CB
   A  36  ASP  CG
   A  36  ASP  OD1
   A  36  ASP  OD2           0.047       0.081       22.02   4.1*sigma

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.041   2242  Z= 0.449
    Angle     :  1.529   6.498   4079  Z= 0.660
    Chirality :  0.079   0.219    176
    Planarity :  0.008   0.047    327
    Dihedral  : 11.127  80.028    769
    Min Nonbonded Distance : 1.482
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  1.61 %
      Favored  : 97.58 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  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: -0.38 (0.70), residues: 137
    helix:  0.11 (0.54), residues: 79
    sheet:  None (None), residues: 0
    loop : -0.62 (0.89), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.015   0.005   PHE A  45 
   TYR   0.068   0.012   TYR A  50 
   ARG   0.039   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.005   PHE A  67 
   TYR   0.056   0.014   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   9.02
  RMS(bonds)            =   0.0032
  RMS(angles)           =   1.08
  MolProbity score      =   1.79

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.53
  MolProbity score      =   1.64

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  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.01, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.1, 64.775, 34.574, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  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: 1105
        1.04 -     1.23: 91
        1.23 -     1.43: 381
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.368 -0.039 1.40e-02 5.10e+03 7.92e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.30e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.90e+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 5.79e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.57e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      101.23 -   106.76: 180
      106.76 -   112.30: 2483
      112.30 -   117.83: 426
      117.83 -   123.37: 812
      123.37 -   128.90: 177
  Bond angle restraints: 4078
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.50    4.10 1.00e+00 1.00e+00 1.68e+01
  angle model="   0" pdb=" 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  118.92    3.68 1.00e+00 1.00e+00 1.35e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
      ideal   model   delta    sigma   weight residual
     116.20  123.43   -7.23 2.00e+00 2.50e-01 1.31e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.92   -3.32 1.00e+00 1.00e+00 1.10e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.88    4.32 1.30e+00 5.92e-01 1.10e+01
  ... (remaining 4073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 956
       17.63 -    35.27: 53
       35.27 -    52.90: 16
       52.90 -    70.54: 5
       70.54 -    88.17: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.39  -38.61     0      5.00e+00 4.00e-02 5.96e+01
  dihedral model="   0" pdb=" CA  LEU A  93 "
           model="   0" pdb=" C   LEU A  93 "
           model="   0" pdb=" N   GLY A  94 "
           model="   0" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.58   25.42     0      5.00e+00 4.00e-02 2.58e+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  157.32   22.68     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.045: 75
       0.045 -    0.090: 45
       0.090 -    0.135: 39
       0.135 -    0.180: 12
       0.180 -    0.225: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality model="   0" pdb=" CA  SER A  97 "
            model="   0" pdb=" N   SER A  97 "
            model="   0" pdb=" C   SER A  97 "
            model="   0" pdb=" CB  SER A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality model="   0" pdb=" CA  TYR A  81 "
            model="   0" pdb=" N   TYR A  81 "
            model="   0" pdb=" C   TYR A  81 "
            model="   0" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.098 2.00e-02 2.50e+03   4.53e-02 6.17e+01
        model="   0" pdb=" CG  TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.094 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.033 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.076 2.00e-02 2.50e+03   3.27e-02 3.21e+01
        model="   0" pdb=" CG  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.016 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 "    0.010 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 "   -0.066 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 "    0.027 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 "    0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.026 2.00e-02 2.50e+03   5.34e-02 2.85e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.092 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.033 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 74
        2.09 -     2.72: 3651
        2.72 -     3.35: 6237
        3.35 -     3.97: 7523
        3.97 -     4.60: 11336
  Nonbonded interactions: 28821
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.465 1.850
  nonbonded model="   0" pdb=" O   THR A  92 "
            model="   0" pdb=" OG  SER A  97 "
     model   vdw
     1.540 2.200
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.619 1.850
  nonbonded model="   0" pdb=" HE1 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.631 2.270
  nonbonded model="   0" pdb=" O   TYR A  81 "
            model="   0" pdb=" HB3 LEU A  93 "
     model   vdw
     1.719 2.620
  ... (remaining 28816 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: 1.04
  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.


============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 69
        1.23 -     1.43: 403
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.75e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.61e+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 7.59e+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 6.99e+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 6.61e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.45 -   106.15: 100
      106.15 -   111.84: 2498
      111.84 -   117.54: 467
      117.54 -   123.23: 815
      123.23 -   128.92: 199
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.38    4.22 1.00e+00 1.00e+00 1.78e+01
  angle model="   0" pdb=" 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  128.54   -6.84 1.80e+00 3.09e-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  119.11    3.49 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     121.70  127.97   -6.27 1.80e+00 3.09e-01 1.21e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.82    4.38 1.30e+00 5.92e-01 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.41: 971
       17.41 -    34.82: 41
       34.82 -    52.23: 15
       52.23 -    69.64: 4
       69.64 -    87.05: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.69   24.31     0      5.00e+00 4.00e-02 2.36e+01
  dihedral model="   0" pdb=" CA  THR A  83 "
           model="   0" pdb=" C   THR A  83 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.35  -18.65     0      5.00e+00 4.00e-02 1.39e+01
  dihedral model="   0" pdb=" C   GLU A  84 "
           model="   0" pdb=" N   GLU A  84 "
           model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" CB  GLU A  84 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.68    8.08     0      2.50e+00 1.60e-01 1.04e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.060: 92
       0.060 -    0.120: 61
       0.120 -    0.179: 18
       0.179 -    0.239: 4
       0.239 -    0.298: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  GLU A  84 "
            model="   0" pdb=" N   GLU A  84 "
            model="   0" pdb=" C   GLU A  84 "
            model="   0" pdb=" CB  GLU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.23e+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 9.83e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.08e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.098 2.00e-02 2.50e+03   4.29e-02 5.51e+01
        model="   0" pdb=" CG  TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.083 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.084 2.00e-02 2.50e+03   3.75e-02 4.21e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.014 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 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.078 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.025 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 "    0.065 2.00e-02 2.50e+03   2.60e-02 2.02e+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 "   -0.008 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 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.08: 59
        2.08 -     2.71: 3516
        2.71 -     3.34: 6292
        3.34 -     3.97: 7643
        3.97 -     4.60: 11346
  Nonbonded interactions: 28856
  Sorted by model distance:
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" HD2 TYR A  91 "
     model   vdw
     1.450 2.270
  nonbonded model="   0" pdb="HG21 ILE A  77 "
            model="   0" pdb=" HD2 TYR A  91 "
     model   vdw
     1.502 2.270
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.669 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.687 1.850
  nonbonded model="   0" pdb=" HE2 TYR A  81 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.736 2.100
  ... (remaining 28851 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Time building chain proxies: 0.95, per 1000 atoms: 0.43
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.78, 58.778, 49.204, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
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 TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.94, per 1000 atoms: 0.42
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (76.366, 42.529, 44.934, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.798)
  Mean delta:    0.012 (Z=  0.636)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   130.12    -8.42  1.80e+00  2.19e+01   4.7*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.79     5.41  1.30e+00  1.73e+01   4.2*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   128.99    -7.29  1.80e+00  1.64e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.422 (Z=  4.679)
  Mean delta:    1.741 (Z=  0.942)

                      ----------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   149.82    30.18  5.00e+00  3.64e+01   6.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   151.66    28.34  5.00e+00  3.21e+01   5.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -152.97   -27.03  5.00e+00  2.92e+01   5.4*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   153.40    26.60  5.00e+00  2.83e+01   5.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   154.34    25.66  5.00e+00  2.63e+01   5.1*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   155.99    24.01  5.00e+00  2.31e+01   4.8*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   156.74    23.26  5.00e+00  2.16e+01   4.7*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   158.80    21.20  5.00e+00  1.80e+01   4.2*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00  -159.52   -20.48  5.00e+00  1.68e+01   4.1*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   159.61    20.39  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.008
  Max. delta:   88.158
  Mean delta:   13.473

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.249
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.453
    Angle     :  1.632   8.604   4079  Z= 0.710
    Chirality :  0.082   0.249    176
    Planarity :  0.008   0.047    327
    Dihedral  : 12.216  89.915    769
    Min Nonbonded Distance : 1.642
  
  Molprobity Statistics.
    All-atom Clashscore : 10.82
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  8.76 %
      Favored  : 87.59 %
    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: -0.34 (0.69), residues: 137
    helix: -0.16 (0.56), residues: 70
    sheet:  None (None), residues: 0
    loop : -0.13 (0.81), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.034   0.006   PHE A  67 
   TYR   0.055   0.009   TYR A 111 
   ARG   0.037   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.020   0.006   PHE A  67 
   TYR   0.046   0.011   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.91 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.722)
  Mean delta:    0.012 (Z=  0.614)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.342 (Z=  3.914)
  Mean delta:    1.604 (Z=  0.873)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   156.19    23.81  5.00e+00  2.27e+01   4.8*sigma

  Min. delta:    0.022
  Max. delta:   75.282
  Mean delta:   12.359

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.201
  Mean delta:    0.076

                       ----------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      :  0.008   0.041   2242  Z= 0.437
    Angle     :  1.544   6.342   4079  Z= 0.667
    Chirality :  0.076   0.201    176
    Planarity :  0.008   0.044    327
    Dihedral  : 11.346  80.022    769
    Min Nonbonded Distance : 1.557
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  6.57 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  2.42 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.51 (0.72), residues: 137
    helix:  0.22 (0.53), residues: 88
    sheet:  None (None), residues: 0
    loop : -1.23 (1.00), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.001   HIS A 139 
   PHE   0.038   0.007   PHE A  15 
   TYR   0.077   0.011   TYR A  50 
   ARG   0.045   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.001   HIS A 139 
   PHE   0.022   0.007   PHE A  15 
   TYR   0.065   0.013   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2217
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2217
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   3.65 %
                favored =  87.59 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =  10.82
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.63
  MolProbity score      =   2.45

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 66
        1.23 -     1.43: 406
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 8.78e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.88e+00
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.034 1.40e-02 5.10e+03 5.87e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.46e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.14e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.05 -   105.83: 76
      105.83 -   111.61: 2443
      111.61 -   117.38: 552
      117.38 -   123.16: 797
      123.16 -   128.93: 211
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.43    4.17 1.00e+00 1.00e+00 1.74e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.03    3.57 1.00e+00 1.00e+00 1.28e+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  126.89    4.31 1.30e+00 5.92e-01 1.10e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.90   -4.50 1.40e+00 5.10e-01 1.03e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
      ideal   model   delta    sigma   weight residual
     116.20  122.49   -6.29 2.00e+00 2.50e-01 9.88e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 973
       18.00 -    36.00: 42
       36.00 -    54.00: 12
       54.00 -    72.00: 4
       72.00 -    89.99: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  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  160.37   19.63     0      5.00e+00 4.00e-02 1.54e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.13   18.87     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 63
       0.036 -    0.073: 47
       0.073 -    0.109: 37
       0.109 -    0.145: 23
       0.145 -    0.182: 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 8.24e-01
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.87e-01
  chirality model="   0" pdb=" CA  ALA A 115 "
            model="   0" pdb=" N   ALA A 115 "
            model="   0" pdb=" C   ALA A 115 "
            model="   0" pdb=" CB  ALA A 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.65   -0.17 2.00e-01 2.50e+01 6.86e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.074 2.00e-02 2.50e+03   3.12e-02 2.92e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.024 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 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.059 2.00e-02 2.50e+03   2.32e-02 1.62e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 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 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.059 2.00e-02 2.50e+03   2.26e-02 1.53e+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 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.020 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 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 149
        2.18 -     2.79: 4358
        2.79 -     3.39: 6197
        3.39 -     4.00: 7600
        4.00 -     4.60: 11452
  Nonbonded interactions: 29756
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ASP A 118 "
            model="   0" pdb=" H   ILE A 122 "
     model   vdw
     1.578 1.850
  nonbonded model="   0" pdb=" HG  SER A  76 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.627 2.100
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.676 1.850
  nonbonded model="   0" pdb=" HG  SER A  17 "
            model="   0" pdb=" OE2 GLU A  84 "
     model   vdw
     1.711 1.850
  nonbonded model="   0" pdb=" O   ILE A 122 "
            model="   0" pdb=" H   VAL A 126 "
     model   vdw
     1.742 1.850
  ... (remaining 29751 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   2.19 %
                favored =  91.24 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.54
  MolProbity score      =   2.10

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.037 (Z=  1.847)
  Mean delta:    0.005 (Z=  0.289)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.956 (Z=  1.652)
  Mean delta:    0.608 (Z=  0.320)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   75.428
  Mean delta:    9.254

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.126
  Mean delta:    0.037

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.015
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.037   2242  Z= 0.206
    Angle     :  1.033   4.956   4079  Z= 0.376
    Chirality :  0.037   0.126    176
    Planarity :  0.002   0.015    327
    Dihedral  :  9.437  88.935    769
    Min Nonbonded Distance : 1.241
  
  Molprobity Statistics.
    All-atom Clashscore : 11.72
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.14 (0.65), residues: 137
    helix: -0.23 (0.55), residues: 70
    sheet:  None (None), residues: 0
    loop :  0.28 (0.71), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.005   0.002   PHE A  67 
   TYR   0.010   0.002   TYR A  12 
   ARG   0.006   0.002   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.007   0.002   TYR A  12 
   ARG   0.004   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  11.72
  RMS(bonds)            =   0.0033
  RMS(angles)           =   1.03
  MolProbity score      =   1.75

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.10
  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.

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (75.312, 39.356, 50.849, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 5
        1.23 -     1.42: 458
        1.42 -     1.61: 669
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.258 -0.027 2.00e-02 2.50e+03 1.81e+00
  bond model="   0" pdb=" C   ARG A 127 "
       model="   0" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.66e+00
  bond model="   0" pdb=" C   ASP A  74 "
       model="   0" pdb=" N   GLU A  75 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.42e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.41e+00
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.313  0.016 1.40e-02 5.10e+03 1.32e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.70 -   106.73: 59
      106.73 -   112.76: 2704
      112.76 -   118.79: 442
      118.79 -   124.83: 832
      124.83 -   130.86: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  123.07   -5.07 3.00e+00 1.11e-01 2.86e+00
  angle model="   0" pdb=" N   ILE A  78 "
        model="   0" pdb=" CA  ILE A  78 "
        model="   0" pdb=" HA  ILE A  78 "
      ideal   model   delta    sigma   weight residual
     110.00  104.96    5.04 3.00e+00 1.11e-01 2.82e+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  104.04    4.96 3.00e+00 1.11e-01 2.73e+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  113.84   -4.84 3.00e+00 1.11e-01 2.61e+00
  angle model="   0" pdb=" N   ILE A  77 "
        model="   0" pdb=" CA  ILE A  77 "
        model="   0" pdb=" HA  ILE A  77 "
      ideal   model   delta    sigma   weight residual
     110.00  105.24    4.76 3.00e+00 1.11e-01 2.51e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 985
       17.27 -    34.55: 22
       34.55 -    51.82: 13
       51.82 -    69.10: 6
       69.10 -    86.37: 7
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" CB  ASP A 118 "
           model="   0" pdb=" CG  ASP A 118 "
           model="   0" pdb=" OD1 ASP A 118 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.67   56.67     1      2.00e+01 2.50e-03 1.08e+01
  dihedral model="   0" pdb=" CA  ASP A  95 "
           model="   0" pdb=" CB  ASP A  95 "
           model="   0" pdb=" CG  ASP A  95 "
           model="   0" pdb=" OD1 ASP A  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.24   56.24     1      2.00e+01 2.50e-03 1.07e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.37  -86.37     1      3.00e+01 1.11e-03 9.99e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 101
       0.029 -    0.057: 59
       0.057 -    0.085: 4
       0.085 -    0.114: 8
       0.114 -    0.142: 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    2.58   -0.14 2.00e-01 2.50e+01 5.06e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.014 2.00e-02 2.50e+03   5.48e-03 9.02e-01
        model="   0" pdb=" CG  TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.000 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 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.013 2.00e-02 2.50e+03   5.43e-03 8.84e-01
        model="   0" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.011 2.00e-02 2.50e+03   4.43e-03 5.89e-01
        model="   0" pdb=" CG  TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.25 -     1.92: 21
        1.92 -     2.59: 2403
        2.59 -     3.26: 6839
        3.26 -     3.93: 8198
        3.93 -     4.60: 12729
  Nonbonded interactions: 30190
  Sorted by model distance:
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" O   TYR A  89 "
     model   vdw
     1.252 2.620
  nonbonded model="   0" pdb=" HD2 TYR A  89 "
            model="   0" pdb="HD21 LEU A  99 "
     model   vdw
     1.494 2.270
  nonbonded model="   0" pdb=" OE2 GLU A  75 "
            model="   0" pdb=" HZ3 LYS A  79 "
     model   vdw
     1.500 1.850
  nonbonded model="   0" pdb=" HE1 PHE A  67 "
            model="   0" pdb="HD13 LEU A  99 "
     model   vdw
     1.569 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  36 "
            model="   0" pdb=" HE2 LYS A  40 "
     model   vdw
     1.638 2.620
  ... (remaining 30185 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.083, 53.316, 60.885, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  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: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.444, 40.837, 64.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (81.482, 56.905, 49.757, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
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 TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.027 (Z=  1.479)
  Mean delta:    0.004 (Z=  0.259)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.738 (Z=  1.634)
  Mean delta:    0.730 (Z=  0.340)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   88.670
  Mean delta:   11.899

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.164
  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   0.027   2242  Z= 0.185
    Angle     :  1.117   5.178   4079  Z= 0.400
    Chirality :  0.042   0.164    176
    Planarity :  0.002   0.026    327
    Dihedral  : 10.845  88.670    769
    Min Nonbonded Distance : 1.451
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.73 %
      Favored  : 99.27 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.80 (0.69), residues: 137
    helix:  0.22 (0.57), residues: 79
    sheet:  None (None), residues: 0
    loop :  1.33 (0.80), residues: 58
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.004   0.001   PHE A  45 
   TYR   0.012   0.003   TYR A  91 
   ARG   0.005   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.009   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: 1.03, per 1000 atoms: 0.46
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (50.476, 40.931, 61.073, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  3.027)
  Mean delta:    0.012 (Z=  0.642)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   116.64    -4.04  1.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.786 (Z=  4.036)
  Mean delta:    1.612 (Z=  0.887)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   150.22    29.78  5.00e+00  3.55e+01   6.0*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   153.70    26.30  5.00e+00  2.77e+01   5.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   158.15    21.85  5.00e+00  1.91e+01   4.4*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   158.87    21.13  5.00e+00  1.79e+01   4.2*sigma

  Min. delta:    0.026
  Max. delta:   84.359
  Mean delta:   12.417

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.203
  Mean delta:    0.078

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.054
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.457
    Angle     :  1.549   6.786   4079  Z= 0.674
    Chirality :  0.078   0.203    176
    Planarity :  0.009   0.042    327
    Dihedral  : 11.338  84.359    769
    Min Nonbonded Distance : 1.530
  
  Molprobity Statistics.
    All-atom Clashscore : 2.71
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  3.65 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  0.81 %
      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: -0.27 (0.69), residues: 137
    helix:  0.08 (0.50), residues: 92
    sheet:  None (None), residues: 0
    loop : -0.45 (0.99), residues: 45
  
  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   0.077   0.011   TYR A  50 
   ARG   0.044   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.063   0.014   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.304, 66.413, 42.372, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   0.00 %
                favored =  99.27 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0031
  RMS(angles)           =   1.12
  MolProbity score      =   1.46

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  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.

  Ramachandran outliers =   4.38 %
                favored =  91.97 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   2.71
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.55
  MolProbity score      =   2.01

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 130
        1.23 -     1.43: 342
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.30e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.19e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.03e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.60e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.29e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.65 -   106.29: 114
      106.29 -   111.92: 2497
      111.92 -   117.56: 459
      117.56 -   123.20: 806
      123.20 -   128.84: 203
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.47    4.13 1.00e+00 1.00e+00 1.71e+01
  angle model="   0" pdb=" CA  ASP A  44 "
        model="   0" pdb=" CB  ASP A  44 "
        model="   0" pdb=" CG  ASP A  44 "
      ideal   model   delta    sigma   weight residual
     112.60  116.58   -3.98 1.00e+00 1.00e+00 1.58e+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  126.29    4.91 1.30e+00 5.92e-01 1.42e+01
  angle model="   0" pdb=" C   SER A  97 "
        model="   0" pdb=" N   SER A  98 "
        model="   0" pdb=" CA  SER A  98 "
      ideal   model   delta    sigma   weight residual
     121.70  128.46   -6.76 1.80e+00 3.09e-01 1.41e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.25    3.35 1.00e+00 1.00e+00 1.12e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.57: 959
       17.57 -    35.14: 57
       35.14 -    52.70: 11
       52.70 -    70.27: 4
       70.27 -    87.84: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.59   27.41     0      5.00e+00 4.00e-02 3.00e+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 -154.13  -25.87     0      5.00e+00 4.00e-02 2.68e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.47   25.53     0      5.00e+00 4.00e-02 2.61e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.055: 84
       0.055 -    0.110: 59
       0.110 -    0.164: 29
       0.164 -    0.218: 3
       0.218 -    0.273: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality model="   0" pdb=" CA  ASP A  74 "
            model="   0" pdb=" N   ASP A  74 "
            model="   0" pdb=" C   ASP A  74 "
            model="   0" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality model="   0" pdb=" 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: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.069 2.00e-02 2.50e+03   3.03e-02 2.75e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.052 2.00e-02 2.50e+03   2.04e-02 1.25e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 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 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.016 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
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.041 2.00e-02 2.50e+03   1.56e-02 7.26e+00
        model="   0" pdb=" CG  TYR A  12 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.020 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 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 117
        2.17 -     2.77: 4129
        2.77 -     3.38: 6069
        3.38 -     3.99: 7164
        3.99 -     4.60: 10968
  Nonbonded interactions: 28447
  Sorted by model distance:
  nonbonded model="   0" pdb="HD23 LEU A 119 "
            model="   0" pdb="HD12 ILE A 122 "
     model   vdw
     1.556 2.440
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.656 1.850
  nonbonded model="   0" pdb=" O   SER A  76 "
            model="   0" pdb=" H   GLY A  80 "
     model   vdw
     1.704 1.850
  nonbonded model="   0" pdb=" O   GLY A  96 "
            model="   0" pdb=" H   SER A  98 "
     model   vdw
     1.725 1.850
  nonbonded model="   0" pdb=" O   LYS A  79 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.740 1.850
  ... (remaining 28442 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2217
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 0.67, per 1000 atoms: 0.30
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.169, 65.761, 55.687, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.08
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 0.63, per 1000 atoms: 0.28
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.577, 49.243, 56.709, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (74.621, 59.856, 42.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 0.67 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 94
        1.23 -     1.43: 378
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.353 -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  1.296  0.034 1.30e-02 5.92e+03 6.91e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.45e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.05e+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 5.96e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.29 -   106.03: 83
      106.03 -   111.77: 2496
      111.77 -   117.51: 496
      117.51 -   123.25: 809
      123.25 -   128.99: 195
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.40    4.20 1.00e+00 1.00e+00 1.76e+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  118.92    3.68 1.00e+00 1.00e+00 1.35e+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  126.61    4.59 1.30e+00 5.92e-01 1.25e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.12   -3.52 1.00e+00 1.00e+00 1.24e+01
  angle model="   0" pdb=" 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 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.35: 955
       16.35 -    32.69: 60
       32.69 -    49.04: 11
       49.04 -    65.39: 5
       65.39 -    81.73: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.46  -16.54     0      5.00e+00 4.00e-02 1.09e+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  164.33   15.67     0      5.00e+00 4.00e-02 9.82e+00
  dihedral model="   0" pdb=" N   ASP A  95 "
           model="   0" pdb=" CA  ASP A  95 "
           model="   0" pdb=" CB  ASP A  95 "
           model="   0" pdb=" CG  ASP A  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.54  -54.46     3      1.50e+01 4.44e-03 9.28e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 73
       0.039 -    0.078: 45
       0.078 -    0.118: 34
       0.118 -    0.157: 20
       0.157 -    0.196: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.58e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.48e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 6.95e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.069 2.00e-02 2.50e+03   2.97e-02 2.65e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.025 2.00e-02 2.50e+03   5.03e-02 2.53e+01
        model="   0" pdb=" CG  ASP A  36 "    0.087 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.030 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.052 2.00e-02 2.50e+03   2.00e-02 1.20e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 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 "   -0.014 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 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.02: 40
        2.02 -     2.67: 3075
        2.67 -     3.31: 6529
        3.31 -     3.96: 7848
        3.96 -     4.60: 11664
  Nonbonded interactions: 29156
  Sorted by model distance:
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" HE2 TYR A  81 "
     model   vdw
     1.380 2.100
  nonbonded model="   0" pdb=" O   TYR A  81 "
            model="   0" pdb=" O   LEU A  93 "
     model   vdw
     1.396 2.800
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.483 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.707 1.850
  nonbonded model="   0" pdb="HD21 LEU A  93 "
            model="   0" pdb="HD13 LEU A  99 "
     model   vdw
     1.721 2.440
  ... (remaining 29151 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2217
  At special positions: 0
  Unit cell: (37.632, 69.64, 77.114, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1105      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 11
        1.23 -     1.42: 452
        1.42 -     1.61: 669
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ILE A 131 "
       model="   0" pdb=" N   LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.40e-02 5.10e+03 2.92e+00
  bond model="   0" pdb=" C   MET A   1 "
       model="   0" pdb=" N   LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.352 -0.023 1.40e-02 5.10e+03 2.66e+00
  bond model="   0" pdb=" C   ILE A  71 "
       model="   0" pdb=" N   ASN A  72 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.60e+00
  bond model="   0" pdb=" C   SER A  76 "
       model="   0" pdb=" N   ILE A  77 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.46e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.41e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.09 -   106.24: 46
      106.24 -   112.40: 2697
      112.40 -   118.56: 451
      118.56 -   124.71: 842
      124.71 -   130.87: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  104.14    4.86 3.00e+00 1.11e-01 2.63e+00
  angle model="   0" pdb=" CB  PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.68   -4.68 3.00e+00 1.11e-01 2.43e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.67   -4.67 3.00e+00 1.11e-01 2.42e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.56   -4.56 3.00e+00 1.11e-01 2.31e+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  105.48    4.52 3.00e+00 1.11e-01 2.27e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 980
       17.86 -    35.72: 23
       35.72 -    53.58: 10
       53.58 -    71.44: 7
       71.44 -    89.30: 13
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.30   89.30     1      3.00e+01 1.11e-03 1.05e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.80  -88.80     1      3.00e+01 1.11e-03 1.04e+01
  dihedral model="   0" pdb=" CB  GLU A 120 "
           model="   0" pdb=" CG  GLU A 120 "
           model="   0" pdb=" CD  GLU A 120 "
           model="   0" pdb=" OE1 GLU A 120 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.72   88.72     1      3.00e+01 1.11e-03 1.04e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.028: 105
       0.028 -    0.055: 52
       0.055 -    0.082: 7
       0.082 -    0.109: 8
       0.109 -    0.136: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  37 "
            model="   0" pdb=" N   ILE A  37 "
            model="   0" pdb=" C   ILE A  37 "
            model="   0" pdb=" CB  ILE A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-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    2.57   -0.14 2.00e-01 2.50e+01 4.57e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.66e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.011 2.00e-02 2.50e+03   5.15e-03 7.96e-01
        model="   0" pdb=" CG  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 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 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 135 "   -0.007 2.00e-02 2.50e+03   5.35e-03 5.72e-01
        model="   0" pdb=" CG  HIS A 135 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 135 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 135 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 135 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 135 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 135 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 135 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.002 2.00e-02 2.50e+03   3.88e-03 4.51e-01
        model="   0" pdb=" CG  TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.07: 64
        2.07 -     2.70: 3633
        2.70 -     3.33: 6440
        3.33 -     3.97: 8112
        3.97 -     4.60: 12540
  Nonbonded interactions: 30789
  Sorted by model distance:
  nonbonded model="   0" pdb="HD11 ILE A  78 "
            model="   0" pdb=" HD2 TYR A  91 "
     model   vdw
     1.433 2.270
  nonbonded model="   0" pdb=" O   ILE A  86 "
            model="   0" pdb=" HH  TYR A  89 "
     model   vdw
     1.564 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.572 1.850
  nonbonded model="   0" pdb="HD12 ILE A  78 "
            model="   0" pdb=" HD2 TYR A  91 "
     model   vdw
     1.573 2.270
  nonbonded model="   0" pdb=" H   GLY A  96 "
            model="   0" pdb=" H   SER A  97 "
     model   vdw
     1.639 2.100
  ... (remaining 30784 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (81.373, 54.529, 48.003, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.277, 57.558, 52.238, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
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 TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.74, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.809, 57.725, 56.551, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  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: 1.02
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  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.

  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (65.387, 52.787, 46.403, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 0.70 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 668
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   THR A  83 "
       model="   0" pdb=" N   GLU A  84 "
    ideal  model  delta    sigma   weight residual
    1.329  1.350 -0.021 1.40e-02 5.10e+03 2.22e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.335 -0.014 1.00e-02 1.00e+04 1.99e+00
  bond model="   0" pdb=" C   TYR A  81 "
       model="   0" pdb=" N   THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.48e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.47e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.35e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.90 -   106.99: 133
      106.99 -   113.08: 2642
      113.08 -   119.17: 436
      119.17 -   125.26: 826
      125.26 -   131.35: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.12   -5.12 3.00e+00 1.11e-01 2.92e+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  104.27    4.73 3.00e+00 1.11e-01 2.48e+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  104.28    4.72 3.00e+00 1.11e-01 2.48e+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  104.35    4.65 3.00e+00 1.11e-01 2.41e+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  113.59   -4.59 3.00e+00 1.11e-01 2.34e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.55: 986
       15.55 -    31.10: 27
       31.10 -    46.66: 8
       46.66 -    62.21: 7
       62.21 -    77.76: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
           model="   0" pdb=" CB  TYR A  91 "
           model="   0" pdb=" CG  TYR A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.11   58.11     3      1.50e+01 4.44e-03 9.46e+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  -77.76   77.76     1      3.00e+01 1.11e-03 8.41e+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  -76.80   76.80     1      3.00e+01 1.11e-03 8.23e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 112
       0.032 -    0.064: 47
       0.064 -    0.096: 12
       0.096 -    0.128: 4
       0.128 -    0.160: 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    2.59   -0.16 2.00e-01 2.50e+01 6.38e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.00e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.014 5.00e-02 4.00e+02   2.14e-02 7.32e-01
        model="   0" pdb=" N   PRO A   6 "   -0.037 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.011 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.012 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  HIS A 139 "    0.004 2.00e-02 2.50e+03   7.49e-03 5.60e-01
        model="   0" pdb=" C   HIS A 139 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" O   HIS A 139 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OXT HIS A 139 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.007 2.00e-02 2.50e+03   4.32e-03 5.60e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.008 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 "   -0.003 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 "    0.002 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 "   -0.002 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 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.09 -     1.79: 8
        1.79 -     2.49: 1584
        2.49 -     3.20: 6960
        3.20 -     3.90: 8269
        3.90 -     4.60: 13189
  Nonbonded interactions: 30010
  Sorted by model distance:
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.089 2.100
  nonbonded model="   0" pdb=" OD2 ASP A 118 "
            model="   0" pdb="HH12 ARG A 127 "
     model   vdw
     1.542 1.850
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" HD2 TYR A  89 "
     model   vdw
     1.554 2.270
  nonbonded model="   0" pdb="HD21 LEU A  93 "
            model="   0" pdb="HD13 LEU A  99 "
     model   vdw
     1.576 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.647 1.850
  ... (remaining 30005 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 1
        1.22 -     1.42: 460
        1.42 -     1.61: 671
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 137 "
       model="   0" pdb=" N   HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.40e-02 5.10e+03 2.73e+00
  bond model="   0" pdb=" C   PRO A  52 "
       model="   0" pdb=" N   LEU A  53 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.015 1.40e-02 5.10e+03 1.11e+00
  bond model="   0" pdb=" C   ASP A  74 "
       model="   0" pdb=" N   GLU A  75 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.015 1.40e-02 5.10e+03 1.11e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.317  0.013 1.30e-02 5.92e+03 1.03e+00
  bond model="   0" pdb=" C   MET A   1 "
       model="   0" pdb=" N   LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.329  1.343 -0.014 1.40e-02 5.10e+03 9.43e-01
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.21 -   106.37: 48
      106.37 -   112.54: 2707
      112.54 -   118.70: 447
      118.70 -   124.86: 835
      124.86 -   131.02: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.93   -4.93 3.00e+00 1.11e-01 2.70e+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  104.36    4.64 3.00e+00 1.11e-01 2.39e+00
  angle model="   0" pdb=" CB  PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.60   -4.60 3.00e+00 1.11e-01 2.35e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.52   -4.52 3.00e+00 1.11e-01 2.27e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.46   -4.46 3.00e+00 1.11e-01 2.21e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 993
       17.60 -    35.20: 15
       35.20 -    52.81: 14
       52.81 -    70.41: 6
       70.41 -    88.01: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A 133 "
           model="   0" pdb=" CG  GLU A 133 "
           model="   0" pdb=" CD  GLU A 133 "
           model="   0" pdb=" OE1 GLU A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.01  -88.01     1      3.00e+01 1.11e-03 1.03e+01
  dihedral model="   0" pdb=" CB  GLU A 123 "
           model="   0" pdb=" CG  GLU A 123 "
           model="   0" pdb=" CD  GLU A 123 "
           model="   0" pdb=" OE1 GLU A 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.31  -87.31     1      3.00e+01 1.11e-03 1.02e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   82.38  -82.38     1      3.00e+01 1.11e-03 9.25e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 127
       0.032 -    0.063: 34
       0.063 -    0.095: 3
       0.095 -    0.127: 10
       0.127 -    0.158: 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    2.59   -0.16 2.00e-01 2.50e+01 6.26e-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    2.58   -0.14 2.00e-01 2.50e+01 5.25e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.014 2.00e-02 2.50e+03   5.41e-03 8.79e-01
        model="   0" pdb=" CG  TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.013 2.00e-02 2.50e+03   5.08e-03 7.73e-01
        model="   0" pdb=" CG  TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 138 "    0.008 2.00e-02 2.50e+03   5.48e-03 6.02e-01
        model="   0" pdb=" CG  HIS A 138 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 138 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 138 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 138 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 138 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 138 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 138 "    0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 144
        2.20 -     2.80: 4615
        2.80 -     3.40: 5717
        3.40 -     4.00: 7382
        4.00 -     4.60: 11186
  Nonbonded interactions: 29044
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ2 LYS A  63 "
            model="   0" pdb=" OD1 ASP A  88 "
     model   vdw
     1.596 1.850
  nonbonded model="   0" pdb=" HB2 PHE A  67 "
            model="   0" pdb=" HE1 TYR A  89 "
     model   vdw
     1.600 2.270
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" HE2 TYR A  89 "
     model   vdw
     1.607 2.100
  nonbonded model="   0" pdb="HG22 ILE A 122 "
            model="   0" pdb=" H   ALA A 124 "
     model   vdw
     1.683 2.270
  nonbonded model="   0" pdb=" HG  SER A  13 "
            model="   0" pdb=" OE1 GLN A  66 "
     model   vdw
     1.693 1.850
  ... (remaining 29039 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: 96
        1.23 -     1.43: 376
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 1.05e+01
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.42e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.35e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.88e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.81e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.07 -   105.85: 72
      105.85 -   111.63: 2457
      111.63 -   117.41: 536
      117.41 -   123.19: 798
      123.19 -   128.97: 216
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.54    4.06 1.00e+00 1.00e+00 1.65e+01
  angle model="   0" pdb=" OE1 GLN A 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 1.29e+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  116.14   -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  126.60    4.60 1.30e+00 5.92e-01 1.25e+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  116.07   -3.47 1.00e+00 1.00e+00 1.21e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.68: 948
       15.68 -    31.37: 56
       31.37 -    47.05: 21
       47.05 -    62.73: 6
       62.73 -    78.42: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  91 "
           model="   0" pdb=" C   TYR A  91 "
           model="   0" pdb=" N   THR A  92 "
           model="   0" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.41   26.59     0      5.00e+00 4.00e-02 2.83e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.50   26.50     0      5.00e+00 4.00e-02 2.81e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.00   23.00     0      5.00e+00 4.00e-02 2.12e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 68
       0.036 -    0.073: 39
       0.073 -    0.109: 39
       0.109 -    0.145: 23
       0.145 -    0.182: 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    2.33    0.18 2.00e-01 2.50e+01 8.24e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.57e-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 6.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.065 2.00e-02 2.50e+03   2.89e-02 2.51e+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 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 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 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.017 2.00e-02 2.50e+03   3.47e-02 1.21e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.060 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.048 2.00e-02 2.50e+03   1.88e-02 1.06e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.030 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 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 163
        2.20 -     2.80: 4325
        2.80 -     3.40: 6015
        3.40 -     4.00: 7184
        4.00 -     4.60: 10734
  Nonbonded interactions: 28421
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.600 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.692 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.738 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.750 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.770 1.850
  ... (remaining 28416 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: 55
        1.23 -     1.42: 417
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 1.05e+01
  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 6.40e+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 6.10e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.94e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.72e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.32 -   106.07: 96
      106.07 -   111.81: 2482
      111.81 -   117.56: 502
      117.56 -   123.31: 801
      123.31 -   129.05: 198
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.40    4.20 1.00e+00 1.00e+00 1.77e+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  116.35   -3.75 1.00e+00 1.00e+00 1.41e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.14   -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  126.74    4.46 1.30e+00 5.92e-01 1.17e+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  119.24    3.36 1.00e+00 1.00e+00 1.13e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 957
       17.04 -    34.08: 53
       34.08 -    51.11: 17
       51.11 -    68.15: 4
       68.15 -    85.19: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.30   41.70     0      5.00e+00 4.00e-02 6.95e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.86   37.14     0      5.00e+00 4.00e-02 5.52e+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  147.27   32.73     0      5.00e+00 4.00e-02 4.29e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.039: 70
       0.039 -    0.077: 38
       0.077 -    0.116: 37
       0.116 -    0.154: 27
       0.154 -    0.192: 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 9.22e-01
  chirality model="   0" pdb=" CA  TYR A  81 "
            model="   0" pdb=" N   TYR A  81 "
            model="   0" pdb=" C   TYR A  81 "
            model="   0" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.03e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.61e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.074 2.00e-02 2.50e+03   3.22e-02 3.11e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.016 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 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.025 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 "   -0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.022 2.00e-02 2.50e+03   4.39e-02 1.93e+01
        model="   0" pdb=" CG  ASP A  36 "    0.076 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.026 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   2.12e-02 1.34e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.035 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 "    0.018 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 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 223
        2.25 -     2.84: 4761
        2.84 -     3.42: 5727
        3.42 -     4.01: 7002
        4.01 -     4.60: 10530
  Nonbonded interactions: 28243
  Sorted by model distance:
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" HD1 TYR A  81 "
     model   vdw
     1.659 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.725 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.731 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.747 1.850
  ... (remaining 28238 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: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.11 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1105
        1.03 -     1.23: 62
        1.23 -     1.43: 410
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   ALA A 115 "
       model="   0" pdb=" N   ASP A 116 "
    ideal  model  delta    sigma   weight residual
    1.329  1.376 -0.047 1.40e-02 5.10e+03 1.15e+01
  bond model="   0" pdb=" N   PRO A 117 "
       model="   0" pdb=" CD  PRO A 117 "
    ideal  model  delta    sigma   weight residual
    1.473  1.436  0.037 1.40e-02 5.10e+03 7.00e+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 6.39e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.30e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.83e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      100.01 -   105.79: 67
      105.79 -   111.58: 2450
      111.58 -   117.36: 541
      117.36 -   123.14: 802
      123.14 -   128.92: 218
  Bond angle restraints: 4078
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.47    4.13 1.00e+00 1.00e+00 1.71e+01
  angle model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     121.70  128.92   -7.22 1.80e+00 3.09e-01 1.61e+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  118.92    3.68 1.00e+00 1.00e+00 1.35e+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  126.47    4.73 1.30e+00 5.92e-01 1.32e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.07   -3.47 1.00e+00 1.00e+00 1.21e+01
  ... (remaining 4073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 967
       17.33 -    34.66: 44
       34.66 -    51.99: 17
       51.99 -    69.32: 3
       69.32 -    86.65: 1
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  130.31   49.69     0      5.00e+00 4.00e-02 9.88e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.94   19.06     0      5.00e+00 4.00e-02 1.45e+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 -161.03  -18.97     0      5.00e+00 4.00e-02 1.44e+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: 32
       0.123 -    0.164: 19
       0.164 -    0.204: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PRO A 117 "
            model="   0" pdb=" N   PRO A 117 "
            model="   0" pdb=" C   PRO A 117 "
            model="   0" pdb=" CB  PRO A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.51    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 9.71e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.46e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 105 "    0.107 2.00e-02 2.50e+03   5.46e-02 8.95e+01
        model="   0" pdb=" CG  TYR A 105 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 105 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 105 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 105 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 105 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 105 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 105 "    0.119 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 105 "   -0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 105 "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 105 "   -0.040 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 105 "   -0.044 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.071 2.00e-02 2.50e+03   3.02e-02 2.74e+01
        model="   0" pdb=" CG  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 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 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 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   2.55e-02 1.95e+01
        model="   0" pdb=" CG  TYR A 111 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 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 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.020 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 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        0.67 -     1.46: 3
        1.46 -     2.24: 255
        2.24 -     3.03: 6621
        3.03 -     3.81: 8808
        3.81 -     4.60: 13982
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 29669
  Sorted by model distance:
  nonbonded model="   0" pdb=" OH  TYR A 105 "
            model="   0" pdb=" HG2 ARG A 127 "
     model   vdw
     0.671 2.620
  nonbonded model="   0" pdb=" HE1 TYR A 105 "
            model="   0" pdb=" HE  ARG A 127 "
     model   vdw
     1.240 2.100
  nonbonded model="   0" pdb=" HA  LYS A 109 "
            model="   0" pdb="HH22 ARG A 127 "
     model   vdw
     1.405 2.270
  nonbonded model="   0" pdb=" HA  VAL A  41 "
            model="   0" pdb="HG22 VAL A 112 "
     model   vdw
     1.539 2.440
  nonbonded model="   0" pdb=" HA  LYS A 109 "
            model="   0" pdb="HH12 ARG A 127 "
     model   vdw
     1.543 2.270
  ... (remaining 29664 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: 0.68
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.80 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.020 (Z=  1.415)
  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:    3.810 (Z=  1.429)
  Mean delta:    0.544 (Z=  0.278)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   89.508
  Mean delta:   16.753

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.145
  Mean delta:    0.041

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.014
  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   0.020   2242  Z= 0.174
    Angle     :  1.024   4.673   4079  Z= 0.365
    Chirality :  0.041   0.145    176
    Planarity :  0.002   0.014    327
    Dihedral  : 13.783  89.508    769
    Min Nonbonded Distance : 1.656
  
  Molprobity Statistics.
    All-atom Clashscore : 7.21
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    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: -1.43 (0.66), residues: 137
    helix: -0.58 (0.57), residues: 70
    sheet:  None (None), residues: 0
    loop : -1.29 (0.73), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.006   0.002   PHE A  67 
   TYR   0.014   0.003   TYR A 111 
   ARG   0.006   0.001   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  67 
   TYR   0.012   0.003   TYR A 111 
   ARG   0.002   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A 137  HIS
   A 139  HIS

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 8
        1.23 -     1.42: 461
        1.42 -     1.62: 663
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.75e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.339 -0.018 1.00e-02 1.00e+04 3.40e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.339 -0.018 1.00e-02 1.00e+04 3.34e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.338 -0.017 1.00e-02 1.00e+04 2.88e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.28e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.82 -   106.60: 70
      106.60 -   112.38: 2658
      112.38 -   118.17: 434
      118.17 -   123.95: 844
      123.95 -   129.73: 73
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   GLY A  80 "
        model="   0" pdb=" N   TYR A  81 "
        model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     121.70  127.59   -5.89 1.80e+00 3.09e-01 1.07e+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  114.99   -2.39 1.00e+00 1.00e+00 5.72e+00
  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  120.77    1.83 1.00e+00 1.00e+00 3.36e+00
  angle model="   0" pdb=" N   TYR A  81 "
        model="   0" pdb=" CA  TYR A  81 "
        model="   0" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     110.00  104.73    5.27 3.00e+00 1.11e-01 3.08e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.80    5.20 3.00e+00 1.11e-01 3.00e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 989
       17.47 -    34.95: 28
       34.95 -    52.42: 7
       52.42 -    69.89: 3
       69.89 -    87.37: 6
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.37  -87.37     1      3.00e+01 1.11e-03 1.02e+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   85.90  -85.90     1      3.00e+01 1.11e-03 9.90e+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   84.26  -84.26     1      3.00e+01 1.11e-03 9.60e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 89
       0.033 -    0.066: 49
       0.066 -    0.098: 32
       0.098 -    0.131: 3
       0.131 -    0.164: 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    2.60   -0.16 2.00e-01 2.50e+01 6.71e-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    2.58   -0.15 2.00e-01 2.50e+01 5.73e-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    2.58   -0.15 2.00e-01 2.50e+01 5.59e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.025 2.00e-02 2.50e+03   1.02e-02 3.11e+00
        model="   0" pdb=" CG  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.022 2.00e-02 2.50e+03   8.52e-03 2.18e+00
        model="   0" pdb=" CG  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.008 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 "    0.003 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 "    0.021 2.00e-02 2.50e+03   7.99e-03 1.91e+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 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 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 "    0.007 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 "   -0.007 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
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 80
        2.15 -     2.76: 4123
        2.76 -     3.37: 5933
        3.37 -     3.99: 7276
        3.99 -     4.60: 11225
  Nonbonded interactions: 28637
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE1 PHE A  15 "
            model="   0" pdb=" HH  TYR A  91 "
     model   vdw
     1.533 2.100
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" OH  TYR A  89 "
     model   vdw
     1.608 1.850
  nonbonded model="   0" pdb=" HB3 TYR A  91 "
            model="   0" pdb="HD12 LEU A  99 "
     model   vdw
     1.612 2.440
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" HH  TYR A  89 "
     model   vdw
     1.613 2.100
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.672 1.850
  ... (remaining 28632 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.67, per 1000 atoms: 0.30
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.098, 61.406, 45.968, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1105
        1.04 -     1.23: 91
        1.23 -     1.43: 381
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2241
  Sorted by residual:
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.368 -0.039 1.40e-02 5.10e+03 7.92e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.30e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.90e+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 5.79e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.57e+00
  ... (remaining 2236 not shown)

  Histogram of bond angle deviations from ideal:
      101.23 -   106.76: 180
      106.76 -   112.30: 2483
      112.30 -   117.83: 426
      117.83 -   123.37: 812
      123.37 -   128.90: 177
  Bond angle restraints: 4078
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.50    4.10 1.00e+00 1.00e+00 1.68e+01
  angle model="   0" pdb=" 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  118.92    3.68 1.00e+00 1.00e+00 1.35e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
      ideal   model   delta    sigma   weight residual
     116.20  123.43   -7.23 2.00e+00 2.50e-01 1.31e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.92   -3.32 1.00e+00 1.00e+00 1.10e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.88    4.32 1.30e+00 5.92e-01 1.10e+01
  ... (remaining 4073 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 956
       17.63 -    35.27: 53
       35.27 -    52.90: 16
       52.90 -    70.54: 5
       70.54 -    88.17: 2
  Dihedral angle restraints: 1032
    sinusoidal: 561
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -141.39  -38.61     0      5.00e+00 4.00e-02 5.96e+01
  dihedral model="   0" pdb=" CA  LEU A  93 "
           model="   0" pdb=" C   LEU A  93 "
           model="   0" pdb=" N   GLY A  94 "
           model="   0" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.58   25.42     0      5.00e+00 4.00e-02 2.58e+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  157.32   22.68     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 1029 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.045: 75
       0.045 -    0.090: 45
       0.090 -    0.135: 39
       0.135 -    0.180: 12
       0.180 -    0.225: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality model="   0" pdb=" CA  SER A  97 "
            model="   0" pdb=" N   SER A  97 "
            model="   0" pdb=" C   SER A  97 "
            model="   0" pdb=" CB  SER A  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality model="   0" pdb=" CA  TYR A  81 "
            model="   0" pdb=" N   TYR A  81 "
            model="   0" pdb=" C   TYR A  81 "
            model="   0" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.098 2.00e-02 2.50e+03   4.53e-02 6.17e+01
        model="   0" pdb=" CG  TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.094 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.033 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.076 2.00e-02 2.50e+03   3.27e-02 3.21e+01
        model="   0" pdb=" CG  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.016 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 "    0.010 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 "   -0.066 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 "    0.027 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 "    0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.026 2.00e-02 2.50e+03   5.34e-02 2.85e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.092 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.033 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.09: 74
        2.09 -     2.72: 3651
        2.72 -     3.35: 6237
        3.35 -     3.97: 7523
        3.97 -     4.60: 11336
  Nonbonded interactions: 28821
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.465 1.850
  nonbonded model="   0" pdb=" O   THR A  92 "
            model="   0" pdb=" OG  SER A  97 "
     model   vdw
     1.540 2.200
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.619 1.850
  nonbonded model="   0" pdb=" HE1 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.631 2.270
  nonbonded model="   0" pdb=" O   TYR A  81 "
            model="   0" pdb=" HB3 LEU A  93 "
     model   vdw
     1.719 2.620
  ... (remaining 28816 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.96, per 1000 atoms: 0.43
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (72.032, 60.139, 40.749, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================

  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.21
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.02
  MolProbity score      =   1.70

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.04 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== 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.


  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
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: 79
        1.23 -     1.43: 393
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.78e+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 6.96e+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 6.04e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.90e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.81e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.00 -   105.81: 74
      105.81 -   111.62: 2452
      111.62 -   117.43: 538
      117.43 -   123.23: 828
      123.23 -   129.04: 187
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.42    4.18 1.00e+00 1.00e+00 1.74e+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  116.20   -3.60 1.00e+00 1.00e+00 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  119.05    3.55 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.84    4.36 1.30e+00 5.92e-01 1.13e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.04   -4.64 1.40e+00 5.10e-01 1.10e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 968
       17.54 -    35.07: 44
       35.07 -    52.61: 16
       52.61 -    70.15: 3
       70.15 -    87.69: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.44   21.56     0      5.00e+00 4.00e-02 1.86e+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  159.58   20.42     0      5.00e+00 4.00e-02 1.67e+01
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.28  -18.72     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 69
       0.044 -    0.088: 49
       0.088 -    0.131: 39
       0.131 -    0.175: 16
       0.175 -    0.219: 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    2.29    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality model="   0" pdb=" CB  THR A  83 "
            model="   0" pdb=" CA  THR A  83 "
            model="   0" pdb=" OG1 THR A  83 "
            model="   0" pdb=" CG2 THR A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.19 2.00e-01 2.50e+01 9.40e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.066 2.00e-02 2.50e+03   2.84e-02 2.41e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 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 "   -0.006 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 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.023 2.00e-02 2.50e+03   4.72e-02 2.23e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.082 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.028 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 1.75e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.44 -     2.07: 58
        2.07 -     2.70: 3429
        2.70 -     3.34: 6335
        3.34 -     3.97: 7515
        3.97 -     4.60: 11347
  Nonbonded interactions: 28684
  Sorted by model distance:
  nonbonded model="   0" pdb="HG21 THR A  83 "
            model="   0" pdb=" HA  THR A  92 "
     model   vdw
     1.440 2.440
  nonbonded model="   0" pdb="HG23 THR A  83 "
            model="   0" pdb=" H   LEU A  93 "
     model   vdw
     1.452 2.270
  nonbonded model="   0" pdb="HG23 THR A  83 "
            model="   0" pdb=" HA  THR A  92 "
     model   vdw
     1.556 2.440
  nonbonded model="   0" pdb=" HA  THR A  83 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     1.606 2.440
  nonbonded model="   0" pdb=" H   THR A  83 "
            model="   0" pdb=" O   LEU A  93 "
     model   vdw
     1.640 1.850
  ... (remaining 28679 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 8.54e+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 8.02e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.367 -0.038 1.40e-02 5.10e+03 7.42e+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 6.62e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.39e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.46 -   106.10: 103
      106.10 -   111.74: 2467
      111.74 -   117.37: 492
      117.37 -   123.01: 778
      123.01 -   128.65: 239
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.64    3.96 1.00e+00 1.00e+00 1.57e+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  126.53    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
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.57    4.63 1.30e+00 5.92e-01 1.27e+01
  angle model="   0" pdb=" 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  126.69    4.51 1.30e+00 5.92e-01 1.21e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.43: 947
       15.43 -    30.86: 59
       30.86 -    46.29: 19
       46.29 -    61.72: 7
       61.72 -    77.15: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.63   32.37     0      5.00e+00 4.00e-02 4.19e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.01   28.99     0      5.00e+00 4.00e-02 3.36e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.28   27.72     0      5.00e+00 4.00e-02 3.07e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 72
       0.039 -    0.078: 38
       0.078 -    0.118: 36
       0.118 -    0.157: 24
       0.157 -    0.196: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 139 "
            model="   0" pdb=" N   HIS A 139 "
            model="   0" pdb=" C   HIS A 139 "
            model="   0" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.46e-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    2.32    0.19 2.00e-01 2.50e+01 9.42e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.075 2.00e-02 2.50e+03   3.00e-02 2.70e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.053 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 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.057 2.00e-02 2.50e+03   2.46e-02 1.81e+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 "    0.012 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 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.046 2.00e-02 2.50e+03   1.78e-02 9.53e+00
        model="   0" pdb=" CG  TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     1.99: 21
        1.99 -     2.64: 2691
        2.64 -     3.29: 6598
        3.29 -     3.95: 7532
        3.95 -     4.60: 11406
  Nonbonded interactions: 28248
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A  49 "
            model="   0" pdb=" HZ3 LYS A 125 "
     model   vdw
     1.334 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.718 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.718 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.818 1.850
  ... (remaining 28243 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.378, 47.584, 54.546, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  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: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.62
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.70 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 62
        1.23 -     1.42: 410
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.13e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.33e+00
  bond model="   0" pdb=" C   THR A  92 "
       model="   0" pdb=" N   LEU A  93 "
    ideal  model  delta    sigma   weight residual
    1.329  1.367 -0.038 1.40e-02 5.10e+03 7.28e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 7.01e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.32e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.15 -   105.89: 88
      105.89 -   111.64: 2438
      111.64 -   117.38: 531
      117.38 -   123.13: 805
      123.13 -   128.87: 217
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.38    4.22 1.00e+00 1.00e+00 1.78e+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  115.24    6.46 1.80e+00 3.09e-01 1.29e+01
  angle model="   0" pdb=" C   GLY A  87 "
        model="   0" pdb=" N   ASP A  88 "
        model="   0" pdb=" CA  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     121.70  128.02   -6.32 1.80e+00 3.09e-01 1.23e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.74    4.46 1.30e+00 5.92e-01 1.18e+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  119.19    3.41 1.00e+00 1.00e+00 1.16e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.05: 956
       17.05 -    34.09: 57
       34.09 -    51.14: 16
       51.14 -    68.19: 3
       68.19 -    85.23: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  135.56   44.44     0      5.00e+00 4.00e-02 7.90e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.60   38.40     0      5.00e+00 4.00e-02 5.90e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.78   30.22     0      5.00e+00 4.00e-02 3.65e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.047: 78
       0.047 -    0.093: 49
       0.093 -    0.139: 39
       0.139 -    0.185: 8
       0.185 -    0.231: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.66e-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    2.33    0.18 2.00e-01 2.50e+01 8.25e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.073 2.00e-02 2.50e+03   3.05e-02 2.80e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.026 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 "   -0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.050 2.00e-02 2.50e+03   1.96e-02 1.16e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  LEU A  93 "    0.016 2.00e-02 2.50e+03   3.25e-02 1.06e+01
        model="   0" pdb=" C   LEU A  93 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" O   LEU A  93 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" N   GLY A  94 "    0.019 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.30: 368
        2.30 -     2.88: 5159
        2.88 -     3.45: 5352
        3.45 -     4.03: 7023
        4.03 -     4.60: 10446
  Nonbonded interactions: 28348
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.730 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.763 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.836 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.844 1.850
  ... (remaining 28343 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Adding C-beta torsion restraints...
  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 -     1.04: 1106
        1.04 -     1.23: 115
        1.23 -     1.43: 358
        1.43 -     1.63: 659
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" N   PRO A 102 "
       model="   0" pdb=" CD  PRO A 102 "
    ideal  model  delta    sigma   weight residual
    1.473  1.428  0.045 1.40e-02 5.10e+03 1.02e+01
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.40e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.02e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.97e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.41e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.76 -   105.65: 62
      105.65 -   111.54: 2444
      111.54 -   117.43: 557
      117.43 -   123.31: 839
      123.31 -   129.20: 177
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.46    4.14 1.00e+00 1.00e+00 1.72e+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  118.92    3.68 1.00e+00 1.00e+00 1.35e+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  116.08   -3.48 1.00e+00 1.00e+00 1.21e+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  127.89   -6.19 1.80e+00 3.09e-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  129.20   -4.80 1.40e+00 5.10e-01 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 961
       17.33 -    34.66: 50
       34.66 -    51.99: 15
       51.99 -    69.32: 6
       69.32 -    86.65: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.47   19.53     0      5.00e+00 4.00e-02 1.53e+01
  dihedral model="   0" pdb=" CA  PRO A 102 "
           model="   0" pdb=" C   PRO A 102 "
           model="   0" pdb=" N   ASP A 103 "
           model="   0" pdb=" CA  ASP A 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.84   16.16     0      5.00e+00 4.00e-02 1.04e+01
  dihedral model="   0" pdb=" N   HIS A 134 "
           model="   0" pdb=" CA  HIS A 134 "
           model="   0" pdb=" CB  HIS A 134 "
           model="   0" pdb=" CG  HIS A 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -125.62  -54.38     3      1.50e+01 4.44e-03 9.28e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 74
       0.042 -    0.083: 45
       0.083 -    0.125: 35
       0.125 -    0.166: 19
       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  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 9.61e-01
  chirality model="   0" pdb=" CG  LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
            model="   0" pdb=" CD1 LEU A  93 "
            model="   0" pdb=" CD2 LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.35e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "   -0.256 2.00e-02 2.50e+03   1.03e-01 3.20e+02
        model="   0" pdb=" CG  PHE A  15 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "    0.062 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "    0.113 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "    0.116 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "   -0.151 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.221 2.00e-02 2.50e+03   1.01e-01 3.03e+02
        model="   0" pdb=" CG  TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.043 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.209 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.085 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.083 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.065 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.120 2.00e-02 2.50e+03   4.95e-02 7.34e+01
        model="   0" pdb=" CG  TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.088 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 91
        2.12 -     2.74: 3878
        2.74 -     3.36: 6204
        3.36 -     3.98: 7499
        3.98 -     4.60: 11357
  Nonbonded interactions: 29029
  Sorted by model distance:
  nonbonded model="   0" pdb="HG13 ILE A  86 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.501 2.270
  nonbonded model="   0" pdb=" HE2 TYR A  89 "
            model="   0" pdb=" HD3 PRO A 102 "
     model   vdw
     1.599 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.667 1.850
  nonbonded model="   0" pdb=" HE2 PHE A  15 "
            model="   0" pdb="HG23 ILE A  86 "
     model   vdw
     1.725 2.270
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.784 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, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ILE A  78 "
       model="   0" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.370 -0.041 1.40e-02 5.10e+03 8.70e+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 6.83e+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 6.41e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.13e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.00e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.39 -   106.04: 90
      106.04 -   111.70: 2476
      111.70 -   117.36: 490
      117.36 -   123.01: 793
      123.01 -   128.67: 230
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  GLY A  80 "
        model="   0" pdb=" C   GLY A  80 "
        model="   0" pdb=" N   TYR A  81 "
      ideal   model   delta    sigma   weight residual
     116.20  124.58   -8.38 2.00e+00 2.50e-01 1.75e+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  118.51    4.09 1.00e+00 1.00e+00 1.67e+01
  angle model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" CA  GLY A  80 "
        model="   0" pdb=" C   GLY A  80 "
      ideal   model   delta    sigma   weight residual
     113.30  124.21  -10.91 2.90e+00 1.19e-01 1.41e+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  126.54    4.66 1.30e+00 5.92e-01 1.28e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.07    3.53 1.00e+00 1.00e+00 1.25e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 968
       17.91 -    35.82: 48
       35.82 -    53.73: 10
       53.73 -    71.63: 6
       71.63 -    89.54: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.88  -28.12     0      5.00e+00 4.00e-02 3.16e+01
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.94   22.06     0      5.00e+00 4.00e-02 1.95e+01
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.92  -21.08     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 86
       0.055 -    0.109: 57
       0.109 -    0.164: 27
       0.164 -    0.218: 3
       0.218 -    0.273: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality model="   0" pdb=" CA  TYR A  81 "
            model="   0" pdb=" N   TYR A  81 "
            model="   0" pdb=" C   TYR A  81 "
            model="   0" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" C   THR A  82 "
            model="   0" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.065 2.00e-02 2.50e+03   2.86e-02 2.45e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 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 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "    0.066 2.00e-02 2.50e+03   2.64e-02 2.08e+01
        model="   0" pdb=" CG  PHE A  15 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "    0.032 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   2.33e-02 1.62e+01
        model="   0" pdb=" CG  TYR A 111 "    0.012 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 "    0.005 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 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 184
        2.22 -     2.81: 4404
        2.81 -     3.41: 5876
        3.41 -     4.00: 7115
        4.00 -     4.60: 10657
  Nonbonded interactions: 28236
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.620 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.689 1.850
  nonbonded model="   0" pdb=" O   GLY A  80 "
            model="   0" pdb=" HA3 GLY A  94 "
     model   vdw
     1.707 2.620
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.756 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.806 1.850
  ... (remaining 28231 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.63, per 1000 atoms: 0.28
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.921, 57.88, 43.411, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.92, per 1000 atoms: 0.41
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.416, 59.042, 64.742, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.91 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.18, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (78.052, 43.649, 48.561, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 99
        1.23 -     1.43: 373
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.07e+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 6.98e+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 6.91e+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 6.69e+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 6.65e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.47 -   106.14: 104
      106.14 -   111.81: 2485
      111.81 -   117.48: 496
      117.48 -   123.16: 781
      123.16 -   128.83: 213
  Bond angle restraints: 4079
  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  118.99    3.61 1.00e+00 1.00e+00 1.30e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.73    4.47 1.30e+00 5.92e-01 1.18e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.35    3.25 1.00e+00 1.00e+00 1.06e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.83   -4.43 1.40e+00 5.10e-01 1.00e+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  127.21    3.99 1.30e+00 5.92e-01 9.43e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 972
       17.83 -    35.66: 42
       35.66 -    53.49: 15
       53.49 -    71.32: 3
       71.32 -    89.15: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.27   27.73     0      5.00e+00 4.00e-02 3.08e+01
  dihedral model="   0" pdb=" CA  ARG A 129 "
           model="   0" pdb=" C   ARG A 129 "
           model="   0" pdb=" N   SER A 130 "
           model="   0" pdb=" CA  SER A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.75   27.25     0      5.00e+00 4.00e-02 2.97e+01
  dihedral model="   0" pdb=" CA  GLU A 133 "
           model="   0" pdb=" C   GLU A 133 "
           model="   0" pdb=" N   HIS A 134 "
           model="   0" pdb=" CA  HIS A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.93   25.07     0      5.00e+00 4.00e-02 2.51e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.040: 77
       0.040 -    0.080: 46
       0.080 -    0.120: 34
       0.120 -    0.160: 16
       0.160 -    0.199: 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 9.95e-01
  chirality model="   0" pdb=" CG  LEU A  39 "
            model="   0" pdb=" CB  LEU A  39 "
            model="   0" pdb=" CD1 LEU A  39 "
            model="   0" pdb=" CD2 LEU A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.74e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.48e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.058 2.00e-02 2.50e+03   2.43e-02 1.77e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.046 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.045 2.00e-02 2.50e+03   2.25e-02 1.51e+01
        model="   0" pdb=" CG  TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.025 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.055 2.00e-02 2.50e+03   2.21e-02 1.46e+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 "   -0.013 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 "    0.039 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 "   -0.017 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
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     1.96: 24
        1.96 -     2.62: 25
  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.22 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

33
        2.62 -     3.28: 6738
        3.28 -     3.94: 7959
        3.94 -     4.60: 12019
  Nonbonded interactions: 29273
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   VAL A  14 "
            model="   0" pdb="HD12 ILE A  86 "
     model   vdw
     1.296 2.620
  nonbonded model="   0" pdb=" O   ILE A  77 "
            model="   0" pdb=" HA3 GLY A  96 "
     model   vdw
     1.611 2.620
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" OE1 GLU A  84 "
     model   vdw
     1.664 2.450
  nonbonded model="   0" pdb=" O   ASP A  95 "
            model="   0" pdb=" H   SER A  98 "
     model   vdw
     1.735 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.735 1.850
  ... (remaining 29268 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 98
        1.23 -     1.43: 374
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 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 8.42e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.46e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.55e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.67e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.34e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.09 -   105.94: 72
      105.94 -   111.79: 2537
      111.79 -   117.63: 464
      117.63 -   123.48: 872
      123.48 -   129.32: 134
  Bond angle restraints: 4079
  Sorted by residual:
  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  126.39    4.81 1.30e+00 5.92e-01 1.37e+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  126.57    4.63 1.30e+00 5.92e-01 1.27e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  119.11    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  126.71    4.49 1.30e+00 5.92e-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  116.03   -3.43 1.00e+00 1.00e+00 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.86: 984
       16.86 -    33.72: 31
       33.72 -    50.58: 11
       50.58 -    67.45: 4
       67.45 -    84.31: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  91 "
           model="   0" pdb=" C   TYR A  91 "
           model="   0" pdb=" N   THR A  92 "
           model="   0" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.63   20.37     0      5.00e+00 4.00e-02 1.66e+01
  dihedral model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" CB  THR A  82 "
           model="   0" pdb=" OG1 THR A  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    9.21   50.79     3      1.50e+01 4.44e-03 8.94e+00
  dihedral model="   0" pdb=" CB  GLU A  49 "
           model="   0" pdb=" CG  GLU A  49 "
           model="   0" pdb=" CD  GLU A  49 "
           model="   0" pdb=" OE1 GLU A  49 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -74.49   74.49     1      3.00e+01 1.11e-03 7.81e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 82
       0.043 -    0.086: 48
       0.086 -    0.129: 32
       0.129 -    0.172: 12
       0.172 -    0.215: 2
  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    2.31    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.20e-01
  chirality model="   0" pdb=" CB  THR A  92 "
            model="   0" pdb=" CA  THR A  92 "
            model="   0" pdb=" OG1 THR A  92 "
            model="   0" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.50e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.060 2.00e-02 2.50e+03   2.56e-02 1.96e+01
        model="   0" pdb=" CG  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.050 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 "    0.022 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 "    0.013 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   2.18e-02 1.43e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 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 "    0.033 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 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.026 2.00e-02 2.50e+03   1.27e-02 4.83e+00
        model="   0" pdb=" CG  TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 37
        2.00 -     2.65: 2841
        2.65 -     3.30: 6664
        3.30 -     3.95: 7923
        3.95 -     4.60: 12152
  Nonbonded interactions: 29617
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE2 PHE A  67 "
            model="   0" pdb=" HD1 TYR A  89 "
     model   vdw
     1.347 2.100
  nonbonded model="   0" pdb=" HB3 TYR A  89 "
            model="   0" pdb=" HD2 LYS A 101 "
     model   vdw
     1.409 2.440
  nonbonded model="   0" pdb="HD13 ILE A  71 "
            model="   0" pdb=" HE1 TYR A  89 "
     model   vdw
     1.510 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.661 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.678 1.850
  ... (remaining 29612 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (46.38, 83.611, 48.016, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.06, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (72.584, 52.684, 43.831, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.96 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)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 102
        1.23 -     1.43: 370
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.88e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.43e+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 5.31e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.27e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.17e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.21 -   106.71: 154
      106.71 -   112.21: 2510
      112.21 -   117.71: 416
      117.71 -   123.21: 802
      123.21 -   128.71: 197
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.38   -3.78 1.00e+00 1.00e+00 1.43e+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 1.24e+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  115.98   -3.38 1.00e+00 1.00e+00 1.14e+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  119.45    3.15 1.00e+00 1.00e+00 9.90e+00
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.71   -4.31 1.40e+00 5.10e-01 9.47e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 976
       17.99 -    35.99: 33
       35.99 -    53.98: 18
       53.98 -    71.97: 5
       71.97 -    89.96: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.39   20.61     0      5.00e+00 4.00e-02 1.70e+01
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.10   18.90     0      5.00e+00 4.00e-02 1.43e+01
  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  161.16   18.84     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 86
       0.054 -    0.108: 57
       0.108 -    0.162: 29
       0.162 -    0.216: 3
       0.216 -    0.270: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.46e-01
  chirality model="   0" pdb=" CA  ASP A  74 "
            model="   0" pdb=" N   ASP A  74 "
            model="   0" pdb=" C   ASP A  74 "
            model="   0" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.19 2.00e-01 2.50e+01 8.57e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.072 2.00e-02 2.50e+03   3.25e-02 3.17e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 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 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.069 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 "   -0.025 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 "   -0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.022 2.00e-02 2.50e+03   4.51e-02 2.04e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.078 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.049 2.00e-02 2.50e+03   1.87e-02 1.05e+01
        model="   0" pdb=" CG  TYR A  12 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.012 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 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 151
        2.19 -     2.79: 4293
        2.79 -     3.40: 6121
        3.40 -     4.00: 7340
        4.00 -     4.60: 10947
  Nonbonded interactions: 28852
  Sorted by model distance:
  nonbonded model="   0" pdb=" HG  SER A  17 "
            model="   0" pdb=" OE2 GLU A  84 "
     model   vdw
     1.590 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.668 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.680 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.744 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.761 1.850
  ... (remaining 28847 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)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  3.019)
  Mean delta:    0.012 (Z=  0.665)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.725 (Z=  3.956)
  Mean delta:    1.658 (Z=  0.895)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.025
  Max. delta:   89.030
  Mean delta:   12.794

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.263
  Mean delta:    0.085

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.052
  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   0.042   2242  Z= 0.473
    Angle     :  1.591  10.925   4079  Z= 0.685
    Chirality :  0.085   0.263    176
    Planarity :  0.008   0.052    327
    Dihedral  : 12.096  89.030    769
    Min Nonbonded Distance : 1.359
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    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 : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.21 (0.66), residues: 137
    helix: -0.82 (0.48), residues: 86
    sheet:  None (None), residues: 0
    loop : -0.44 (0.89), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.013   0.003   PHE A  67 
   TYR   0.066   0.009   TYR A  50 
   ARG   0.038   0.008   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.013   0.003   PHE A  67 
   TYR   0.054   0.011   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   7.66
  RMS(bonds)            =   0.0088
  RMS(angles)           =   1.59
  MolProbity score      =   1.87

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== Collecting inputs ==============================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.378, 56.036, 49.61, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 117
        1.23 -     1.43: 355
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.07e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.20e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.48e+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 6.33e+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 5.62e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.98 -   105.83: 70
      105.83 -   111.68: 2477
      111.68 -   117.53: 524
      117.53 -   123.38: 837
      123.38 -   129.23: 171
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.79    3.81 1.00e+00 1.00e+00 1.45e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.23   -3.63 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" 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  126.66    4.54 1.30e+00 5.92e-01 1.22e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.23   -4.83 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  116.04   -3.44 1.00e+00 1.00e+00 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 964
       16.80 -    33.60: 45
       33.60 -    50.40: 14
       50.40 -    67.20: 8
       67.20 -    84.00: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.51   35.49     0      5.00e+00 4.00e-02 5.04e+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  155.69   24.31     0      5.00e+00 4.00e-02 2.36e+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  159.77   20.23     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.040: 72
       0.040 -    0.080: 46
       0.080 -    0.119: 34
       0.119 -    0.159: 19
       0.159 -    0.198: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.85e-01
  chirality model="   0" pdb=" CA  PRO A 117 "
            model="   0" pdb=" N   PRO A 117 "
            model="   0" pdb=" C   PRO A 117 "
            model="   0" pdb=" CB  PRO A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.42e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.024 2.00e-02 2.50e+03   4.83e-02 2.34e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.084 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.029 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.063 2.00e-02 2.50e+03   2.72e-02 2.22e+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 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.058 2.00e-02 2.50e+03   2.29e-02 1.57e+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 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.05: 56
        2.05 -     2.69: 3383
        2.69 -     3.33: 6539
        3.33 -     3.96: 7964
        3.96 -     4.60: 12058
  Nonbonded interactions: 30000
  Sorted by model distance:
  nonbonded model="   0" pdb=" HH  TYR A  89 "
            model="   0" pdb=" O   ASP A 103 "
     model   vdw
     1.418 1.850
  nonbonded model="   0" pdb=" HD3 LYS A  63 "
            model="   0" pdb=" HE2 TYR A  89 "
     model   vdw
     1.443 2.270
  nonbonded model="   0" pdb="HE22 GLN A  66 "
            model="   0" pdb="HG21 ILE A  86 "
     model   vdw
     1.505 2.270
  nonbonded model="   0" pdb=" HE2 PHE A  15 "
            model="   0" pdb="HD11 ILE A  86 "
     model   vdw
     1.514 2.270
  nonbonded model="   0" pdb=" HZ  PHE A  15 "
            model="   0" pdb=" OH  TYR A  91 "
     model   vdw
     1.538 2.450
  ... (remaining 29995 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.93, per 1000 atoms: 0.42
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.345, 69.311, 42.229, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 0.75, per 1000 atoms: 0.34
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.992, 66.693, 60.071, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 79
        1.23 -     1.43: 393
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 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 8.19e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.55e+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 5.88e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.80e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.24e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.95 -   105.70: 70
      105.70 -   111.46: 2413
      111.46 -   117.22: 563
      117.22 -   122.98: 791
      122.98 -   128.74: 242
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.61    3.99 1.00e+00 1.00e+00 1.59e+01
  angle model="   0" pdb=" C   THR A  82 "
        model="   0" pdb=" N   THR A  83 "
        model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  128.37   -6.67 1.80e+00 3.09e-01 1.37e+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  116.26   -3.66 1.00e+00 1.00e+00 1.34e+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  126.61    4.59 1.30e+00 5.92e-01 1.25e+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  119.09    3.51 1.00e+00 1.00e+00 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 969
       17.84 -    35.68: 44
       35.68 -    53.52: 14
       53.52 -    71.35: 4
       71.35 -    89.19: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.80   32.20     0      5.00e+00 4.00e-02 4.15e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.21   25.79     0      5.00e+00 4.00e-02 2.66e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  165.54   14.46     0      5.00e+00 4.00e-02 8.36e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 68
       0.038 -    0.076: 42
       0.076 -    0.113: 38
       0.113 -    0.151: 24
       0.151 -    0.189: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.91e-01
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.12e-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 7.23e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.115 2.00e-02 2.50e+03   4.75e-02 6.77e+01
        model="   0" pdb=" CG  TYR A  89 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.086 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.072 2.00e-02 2.50e+03   3.19e-02 3.05e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.019 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  91 "    0.057 2.00e-02 2.50e+03   2.93e-02 2.57e+01
        model="   0" pdb=" CG  TYR A  91 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.064 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 137
        2.19 -     2.79: 4241
        2.79 -     3.39: 6044
        3.39 -     4.00: 7163
        4.00 -     4.60: 10880
  Nonbonded interactions: 28465
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.584 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.689 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.753 1.850
  nonbonded model="   0" pdb="HD23 LEU A 119 "
            model="   0" pdb="HD12 ILE A 122 "
     model   vdw
     1.755 2.440
  nonbonded model="   0" pdb="HD11 LEU A  64 "
            model="   0" pdb=" HE3 LYS A 101 "
     model   vdw
     1.759 2.440
  ... (remaining 28460 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.15 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.78
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.91 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 668
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ILE A  86 "
       model="   0" pdb=" N   GLY A  87 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.32e+00
  bond model="   0" pdb=" C   VAL A 126 "
       model="   0" pdb=" N   ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.93e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.335 -0.014 1.00e-02 1.00e+04 1.88e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.308  0.013 1.00e-02 1.00e+04 1.74e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.42e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.47 -   106.61: 56
      106.61 -   112.76: 2711
      112.76 -   118.91: 439
      118.91 -   125.05: 831
      125.05 -   131.20: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CG  ARG A 129 "
        model="   0" pdb=" CD  ARG A 129 "
        model="   0" pdb=" NE  ARG A 129 "
      ideal   model   delta    sigma   weight residual
     112.00  115.80   -3.80 2.20e+00 2.07e-01 2.98e+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  104.06    4.94 3.00e+00 1.11e-01 2.72e+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  113.94   -4.94 3.00e+00 1.11e-01 2.71e+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  104.11    4.89 3.00e+00 1.11e-01 2.66e+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 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.44: 986
       16.44 -    32.88: 28
       32.88 -    49.32: 12
       49.32 -    65.77: 4
       65.77 -    82.21: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLU A  84 "
           model="   0" pdb=" CB  GLU A  84 "
           model="   0" pdb=" CG  GLU A  84 "
           model="   0" pdb=" CD  GLU A  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.16   57.84     3      1.50e+01 4.44e-03 9.45e+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
     -60.00   -3.46  -56.54     3      1.50e+01 4.44e-03 9.40e+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  -75.61   75.61     1      3.00e+01 1.11e-03 8.02e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 97
       0.028 -    0.056: 57
       0.056 -    0.084: 11
       0.084 -    0.111: 7
       0.111 -    0.139: 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   -0.14 2.00e-01 2.50e+01 4.85e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.37e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.016 5.00e-02 4.00e+02   2.48e-02 9.85e-01
        model="   0" pdb=" N   PRO A   6 "   -0.043 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.013 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.014 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.008 2.00e-02 2.50e+03   4.34e-03 5.65e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.010 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 "   -0.000 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 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  GLY A  87 "    0.003 2.00e-02 2.50e+03   6.71e-03 4.51e-01
        model="   0" pdb=" C   GLY A  87 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" O   GLY A  87 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" N   ASP A  88 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.68 -     2.26: 264
        2.26 -     2.85: 5118
        2.85 -     3.43: 5457
        3.43 -     4.02: 7401
        4.02 -     4.60: 11194
  Nonbonded interactions: 29434
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   GLU A  84 "
            model="   0" pdb=" HG  SER A  90 "
     model   vdw
     1.680 1.850
  nonbonded model="   0" pdb=" HE1 MET A   1 "
            model="   0" pdb=" HB2 ASP A  44 "
     model   vdw
     1.742 2.440
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" HD1 TYR A  91 "
     model   vdw
     1.781 2.270
  nonbonded model="   0" pdb=" HG2 GLU A  32 "
            model="   0" pdb="HH12 ARG A 129 "
     model   vdw
     1.786 2.270
  nonbonded model="   0" pdb=" HB3 LEU A   3 "
            model="   0" pdb="HD11 LEU A  53 "
     model   vdw
     1.799 2.440
  ... (remaining 29429 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.09
  Adding C-beta torsion restraints...
  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: 98
        1.23 -     1.43: 374
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.42e+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 8.03e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.26e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.23e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.72e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.64 -   106.28: 117
      106.28 -   111.91: 2493
      111.91 -   117.55: 464
      117.55 -   123.18: 798
      123.18 -   128.82: 207
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.54    4.06 1.00e+00 1.00e+00 1.65e+01
  angle model="   0" pdb=" 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  116.25   -3.65 1.00e+00 1.00e+00 1.33e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.10    3.50 1.00e+00 1.00e+00 1.23e+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  126.77    4.43 1.30e+00 5.92e-01 1.16e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.00   -3.40 1.00e+00 1.00e+00 1.16e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 965
       16.87 -    33.74: 41
       33.74 -    50.60: 20
       50.60 -    67.47: 4
       67.47 -    84.34: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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 -149.19  -30.81     0      5.00e+00 4.00e-02 3.80e+01
  dihedral model="   0" pdb=" CA  ARG A 129 "
           model="   0" pdb=" C   ARG A 129 "
           model="   0" pdb=" N   SER A 130 "
           model="   0" pdb=" CA  SER A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.29   26.71     0      5.00e+00 4.00e-02 2.85e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.86   25.14     0      5.00e+00 4.00e-02 2.53e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 77
       0.047 -    0.093: 46
       0.093 -    0.139: 40
       0.139 -    0.186: 11
       0.186 -    0.232: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.67   -0.23 2.00e-01 2.50e+01 1.34e+00
  chirality model="   0" pdb=" CA  GLU A 120 "
            model="   0" pdb=" N   GLU A 120 "
            model="   0" pdb=" C   GLU A 120 "
            model="   0" pdb=" CB  GLU A 120 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 8.71e-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 7.77e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.071 2.00e-02 2.50e+03   3.16e-02 3.00e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.066 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 "   -0.022 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 "   -0.021 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.066 2.00e-02 2.50e+03   2.64e-02 2.09e+01
        model="   0" pdb=" CG  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.020 2.00e-02 2.50e+03   4.19e-02 1.76e+01
        model="   0" pdb=" CG  ASP A  36 "    0.072 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.35 -     2.00: 29
        2.00 -     2.65: 2798
        2.65 -     3.30: 6535
        3.30 -     3.95: 7406
        3.95 -     4.60: 11191
  Nonbonded interactions: 27959
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE3 MET A   1 "
            model="   0" pdb="HD21 LEU A   3 "
     model   vdw
     1.346 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.428 1.850
  nonbonded model="   0" pdb="HD11 LEU A 119 "
            model="   0" pdb="HH21 ARG A 127 "
     model   vdw
     1.627 2.270
  nonbonded model="   0" pdb="HD21 LEU A 119 "
            model="   0" pdb="HH21 ARG A 127 "
     model   vdw
     1.642 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.702 1.850
  ... (remaining 27954 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.08 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 6
        1.23 -     1.42: 458
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ILE A  51 "
       model="   0" pdb=" N   PRO A  52 "
    ideal  model  delta    sigma   weight residual
    1.341  1.314  0.027 1.60e-02 3.91e+03 2.93e+00
  bond model="   0" pdb=" C   ARG A 127 "
       model="   0" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.16e+00
  bond model="   0" pdb=" C   GLY A 121 "
       model="   0" pdb=" N   ILE A 122 "
    ideal  model  delta    sigma   weight residual
    1.329  1.310  0.019 1.40e-02 5.10e+03 1.93e+00
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.72e+00
  bond model="   0" pdb=" C   ILE A 131 "
       model="   0" pdb=" N   LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.68e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.20 -   106.36: 44
      106.36 -   112.51: 2745
      112.51 -   118.67: 409
      118.67 -   124.82: 837
      124.82 -   130.98: 44
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  HIS A 137 "
        model="   0" pdb=" CB  HIS A 137 "
        model="   0" pdb=" CG  HIS A 137 "
      ideal   model   delta    sigma   weight residual
     113.80  112.13    1.67 1.00e+00 1.00e+00 2.80e+00
  angle model="   0" pdb=" CA  HIS A 138 "
        model="   0" pdb=" CB  HIS A 138 "
        model="   0" pdb=" CG  HIS A 138 "
      ideal   model   delta    sigma   weight residual
     113.80  112.23    1.57 1.00e+00 1.00e+00 2.45e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.65   -4.65 3.00e+00 1.11e-01 2.40e+00
  angle model="   0" pdb=" CA  HIS A 135 "
        model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
      ideal   model   delta    sigma   weight residual
     113.80  112.29    1.51 1.00e+00 1.00e+00 2.28e+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  113.50   -4.50 3.00e+00 1.11e-01 2.25e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.44: 992
       15.44 -    30.88: 25
       30.88 -    46.32: 14
       46.32 -    61.76: 1
       61.76 -    77.19: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -77.19   77.19     2      3.00e+01 1.11e-03 5.07e+00
  dihedral model="   0" pdb=" CA  ASP A 110 "
           model="   0" pdb=" CB  ASP A 110 "
           model="   0" pdb=" CG  ASP A 110 "
           model="   0" pdb=" OD1 ASP A 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
      70.00   35.37   34.63     1      2.00e+01 2.50e-03 4.25e+00
  dihedral model="   0" pdb=" CA  ASP A  36 "
           model="   0" pdb=" CB  ASP A  36 "
           model="   0" pdb=" CG  ASP A  36 "
           model="   0" pdb=" OD1 ASP A  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
      70.00   37.08   32.92     1      2.00e+01 2.50e-03 3.85e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.031: 124
       0.031 -    0.061: 34
       0.061 -    0.091: 7
       0.091 -    0.122: 9
       0.122 -    0.152: 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    2.59   -0.15 2.00e-01 2.50e+01 5.77e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.04e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.58e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CD  ARG A  58 "   -0.017 9.50e-02 1.11e+02   7.58e-03 5.95e-01
        model="   0" pdb=" NE  ARG A  58 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  ARG A  58 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" NH1 ARG A  58 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" NH2 ARG A  58 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb="HH11 ARG A  58 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb="HH12 ARG A  58 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb="HH21 ARG A  58 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb="HH22 ARG A  58 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "   -0.011 5.00e-02 4.00e+02   1.73e-02 4.81e-01
        model="   0" pdb=" N   PRO A  54 "    0.030 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "   -0.009 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "   -0.010 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.009 2.00e-02 2.50e+03   3.89e-03 4.54e-01
        model="   0" pdb=" CG  TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.44 -     2.07: 38
        2.07 -     2.70: 3764
        2.70 -     3.34: 5740
        3.34 -     3.97: 7134
        3.97 -     4.60: 11029
  Nonbonded interactions: 27705
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.438 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.634 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.674 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.694 1.850
  nonbonded model="   0" pdb="HD12 ILE A  37 "
            model="   0" pdb="HD23 LEU A  61 "
     model   vdw
     1.699 2.440
  ... (remaining 27700 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   GLY A  80 "
       model="   0" pdb=" N   TYR A  81 "
    ideal  model  delta    sigma   weight residual
    1.329  1.308  0.021 1.40e-02 5.10e+03 2.28e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.11e+00
  bond model="   0" pdb=" C   HIS A 135 "
       model="   0" pdb=" N   HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+03 1.73e+00
  bond model="   0" pdb=" CD2 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.374  1.386 -0.012 1.10e-02 8.26e+03 1.26e+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 1.11e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.22 -   106.38: 46
      106.38 -   112.54: 2712
      112.54 -   118.70: 444
      118.70 -   124.86: 834
      124.86 -   131.02: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.87    5.13 3.00e+00 1.11e-01 2.92e+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  113.97   -4.97 3.00e+00 1.11e-01 2.74e+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  104.17    4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.48   -4.48 3.00e+00 1.11e-01 2.23e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.32   -4.32 3.00e+00 1.11e-01 2.07e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 985
       16.01 -    32.02: 29
       32.02 -    48.03: 12
       48.03 -    64.04: 3
       64.04 -    80.05: 4
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   69.42  -69.42     1      3.00e+01 1.11e-03 6.92e+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   67.80  -67.80     1      3.00e+01 1.11e-03 6.64e+00
  dihedral model="   0" pdb=" CE1 TYR A  50 "
           model="   0" pdb=" CZ  TYR A  50 "
           model="   0" pdb=" OH  TYR A  50 "
           model="   0" pdb=" HH  TYR A  50 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00   99.95   80.05     2      3.00e+01 1.11e-03 5.17e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 113
       0.028 -    0.055: 46
       0.055 -    0.083: 6
       0.083 -    0.110: 8
       0.110 -    0.138: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.74e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.65e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.55e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.015 5.00e-02 4.00e+02   2.34e-02 8.75e-01
        model="   0" pdb=" N   PRO A   6 "   -0.040 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.013 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.009 2.00e-02 2.50e+03   4.22e-03 5.35e-01
        model="   0" pdb=" CG  TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   LEU A  53 "   -0.012 5.00e-02 4.00e+02   1.79e-02 5.15e-01
        model="   0" pdb=" N   PRO A  54 "    0.031 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A  54 "   -0.009 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A  54 "   -0.010 5.00e-02 4.00e+02
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 195
        2.23 -     2.82: 4829
        2.82 -     3.41: 5826
        3.41 -     4.01: 7529
        4.01 -     4.60: 11394
  Nonbonded interactions: 29773
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.633 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  63 "
            model="   0" pdb=" OD2 ASP A  88 "
     model   vdw
     1.646 1.850
  nonbonded model="   0" pdb=" HB3 ALA A  48 "
            model="   0" pdb="HH11 ARG A 127 "
     model   vdw
     1.695 2.270
  nonbonded model="   0" pdb="HD13 LEU A  93 "
            model="   0" pdb=" HA2 GLY A  96 "
     model   vdw
     1.748 2.440
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.782 2.270
  ... (remaining 29768 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 0.80, per 1000 atoms: 0.36
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.992, 66.693, 60.071, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.06, per 1000 atoms: 0.48
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.574, 63.057, 59.89, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.019 (Z=  1.434)
  Mean delta:    0.004 (Z=  0.241)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.838 (Z=  1.613)
  Mean delta:    0.599 (Z=  0.298)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.004
  Max. delta:   83.252
  Mean delta:   11.579

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.148
  Mean delta:    0.040

                       ----------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   0.019   2242  Z= 0.172
    Angle     :  1.047   4.838   4079  Z= 0.375
    Chirality :  0.040   0.148    176
    Planarity :  0.002   0.021    327
    Dihedral  : 11.182  83.252    769
    Min Nonbonded Distance : 1.389
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.23 (0.66), residues: 137
    helix: -0.46 (0.56), residues: 68
    sheet:  None (None), residues: 0
    loop :  0.39 (0.73), residues: 69
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.005   0.002   PHE A  15 
   TYR   0.015   0.002   TYR A  12 
   ARG   0.005   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 135 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.011   0.002   TYR A  12 
   ARG   0.001   0.000   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
  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 =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0028
  RMS(angles)           =   1.05
  MolProbity score      =   1.61

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 110
        1.23 -     1.43: 362
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.02e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.50e+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 7.14e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 5.99e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.91e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.08 -   106.64: 153
      106.64 -   112.19: 2508
      112.19 -   117.75: 419
      117.75 -   123.31: 815
      123.31 -   128.86: 184
  Bond angle restraints: 4079
  Sorted by residual:
  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  116.33   -3.73 1.00e+00 1.00e+00 1.39e+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  118.88    3.72 1.00e+00 1.00e+00 1.38e+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 1.24e+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=" 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  126.67    4.53 1.30e+00 5.92e-01 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 967
       17.76 -    35.52: 49
       35.52 -    53.28: 10
       53.28 -    71.04: 5
       71.04 -    88.80: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  85 "
           model="   0" pdb=" C   LYS A  85 "
           model="   0" pdb=" N   ILE A  86 "
           model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.95   27.05     0      5.00e+00 4.00e-02 2.93e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.84   23.16     0      5.00e+00 4.00e-02 2.15e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.15   17.85     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 67
       0.039 -    0.077: 46
       0.077 -    0.116: 35
       0.116 -    0.154: 21
       0.154 -    0.193: 7
  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 9.29e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.15e-01
  chirality model="   0" pdb=" CA  LEU A 119 "
            model="   0" pdb=" N   LEU A 119 "
            model="   0" pdb=" C   LEU A 119 "
            model="   0" pdb=" CB  LEU A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.74e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.065 2.00e-02 2.50e+03   2.81e-02 2.37e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 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 "   -0.004 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 "    0.021 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 "    0.015 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.023 2.00e-02 2.50e+03   4.69e-02 2.20e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.081 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.028 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.066 2.00e-02 2.50e+03   2.60e-02 2.03e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 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 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     1.96: 23
        1.96 -     2.62: 2526
        2.62 -     3.28: 6784
        3.28 -     3.94: 7818
        3.94 -     4.60: 11783
  Nonbonded interactions: 28934
  Sorted by model distance:
  nonbonded model="   0" pdb="HD21 LEU A  39 "
            model="   0" pdb=" HG3 GLU A 123 "
     model   vdw
     1.303 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.621 1.850
  nonbonded model="   0" pdb="HG21 VAL A  14 "
            model="   0" pdb="HG23 ILE A  86 "
     model   vdw
     1.701 2.440
  nonbonded model="   0" pdb=" HB3 SER A  17 "
            model="   0" pdb="HG21 ILE A  77 "
     model   vdw
     1.726 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.732 1.850
  ... (remaining 28929 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: 0.83
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.96 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 120
        1.23 -     1.43: 352
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.32e+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 6.66e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.70e+00
  bond model="   0" pdb=" CE1 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.54e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.27e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.41 -   106.09: 92
      106.09 -   111.77: 2490
      111.77 -   117.44: 484
      117.44 -   123.12: 802
      123.12 -   128.80: 211
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.64    3.96 1.00e+00 1.00e+00 1.56e+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  118.83    3.77 1.00e+00 1.00e+00 1.42e+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
  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  115.93   -3.33 1.00e+00 1.00e+00 1.11e+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  115.80   -3.20 1.00e+00 1.00e+00 1.03e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 967
       17.78 -    35.55: 46
       35.55 -    53.33: 15
       53.33 -    71.11: 4
       71.11 -    88.88: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.10   21.90     0      5.00e+00 4.00e-02 1.92e+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  160.18   19.82     0      5.00e+00 4.00e-02 1.57e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.64   19.36     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.048: 83
       0.048 -    0.095: 43
       0.095 -    0.142: 37
       0.142 -    0.189: 11
       0.189 -    0.236: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    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    2.31    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   -2.76    0.17 2.00e-01 2.50e+01 6.87e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.139 2.00e-02 2.50e+03   5.98e-02 1.07e+02
        model="   0" pdb=" CG  TYR A  81 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.117 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.032 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.025 2.00e-02 2.50e+03   5.20e-02 2.70e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.090 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.032 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.058 2.00e-02 2.50e+03   2.59e-02 2.01e+01
        model="   0" pdb=" CG  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.20: 147
        2.20 -     2.80: 4332
        2.80 -     3.40: 6021
        3.40 -     4.00: 7199
        4.00 -     4.60: 10938
  Nonbonded interactions: 28637
  Sorted by model distance:
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" OE1 GLU A  84 "
     model   vdw
     1.594 2.450
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.598 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.618 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.647 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.722 1.850
  ... (remaining 28632 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: 77
        1.23 -     1.43: 395
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.11e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.48e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.26e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.89e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.69e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.31 -   106.03: 91
      106.03 -   111.76: 2490
      111.76 -   117.48: 480
      117.48 -   123.20: 823
      123.20 -   128.92: 195
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.44    4.16 1.00e+00 1.00e+00 1.73e+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  126.23    4.97 1.30e+00 5.92e-01 1.46e+01
  angle model="   0" pdb=" C   THR A  82 "
        model="   0" pdb=" N   THR A  83 "
        model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  128.45   -6.75 1.80e+00 3.09e-01 1.41e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.37    4.83 1.30e+00 5.92e-01 1.38e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.38    4.82 1.30e+00 5.92e-01 1.37e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 967
       17.32 -    34.64: 45
       34.64 -    51.96: 15
       51.96 -    69.28: 5
       69.28 -    86.60: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.66  -25.34     0      5.00e+00 4.00e-02 2.57e+01
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.74  -24.26     0      5.00e+00 4.00e-02 2.35e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.76   24.24     0      5.00e+00 4.00e-02 2.35e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 73
       0.040 -    0.079: 45
       0.079 -    0.119: 33
       0.119 -    0.158: 19
       0.158 -    0.198: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.78e-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 7.76e-01
  chirality model="   0" pdb=" CA  TYR A  89 "
            model="   0" pdb=" N   TYR A  89 "
            model="   0" pdb=" C   TYR A  89 "
            model="   0" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.87e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.107 2.00e-02 2.50e+03   4.54e-02 6.17e+01
        model="   0" pdb=" CG  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.084 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.021 2.00e-02 2.50e+03   4.18e-02 1.75e+01
        model="   0" pdb=" CG  ASP A  36 "    0.072 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.025 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.057 2.00e-02 2.50e+03   2.25e-02 1.51e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 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 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 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 "    0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.19: 145
        2.19 -     2.79: 4257
        2.79 -     3.39: 6005
        3.39 -     4.00: 7170
        4.00 -     4.60: 10793
  Nonbonded interactions: 28370
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.587 1.850
  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=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.725 1.850
  nonbonded model="   0" pdb=" OH  TYR A  81 "
            model="   0" pdb=" HG1 THR A  92 "
     model   vdw
     1.742 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.751 1.850
  ... (remaining 28365 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.74
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.84 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: 120
        1.23 -     1.43: 352
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.32e+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 6.66e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.70e+00
  bond model="   0" pdb=" CE1 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.54e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.27e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.41 -   106.09: 92
      106.09 -   111.77: 2490
      111.77 -   117.44: 484
      117.44 -   123.12: 802
      123.12 -   128.80: 211
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.64    3.96 1.00e+00 1.00e+00 1.56e+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  118.83    3.77 1.00e+00 1.00e+00 1.42e+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
  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  115.93   -3.33 1.00e+00 1.00e+00 1.11e+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  115.80   -3.20 1.00e+00 1.00e+00 1.03e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 967
       17.78 -    35.55: 46
       35.55 -    53.33: 15
       53.33 -    71.11: 4
       71.11 -    88.88: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.10   21.90     0      5.00e+00 4.00e-02 1.92e+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  160.18   19.82     0      5.00e+00 4.00e-02 1.57e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.64   19.36     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.048: 83
       0.048 -    0.095: 43
       0.095 -    0.142: 37
       0.142 -    0.189: 11
       0.189 -    0.236: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    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    2.31    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   -2.76    0.17 2.00e-01 2.50e+01 6.87e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.139 2.00e-02 2.50e+03   5.98e-02 1.07e+02
        model="   0" pdb=" CG  TYR A  81 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.117 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.050 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.032 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.025 2.00e-02 2.50e+03   5.20e-02 2.70e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.090 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.032 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.058 2.00e-02 2.50e+03   2.59e-02 2.01e+01
        model="   0" pdb=" CG  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.20: 147
        2.20 -     2.80: 4332
        2.80 -     3.40: 6021
        3.40 -     4.00: 7199
        4.00 -     4.60: 10938
  Nonbonded interactions: 28637
  Sorted by model distance:
  nonbonded model="   0" pdb=" HD1 PHE A  15 "
            model="   0" pdb=" OE1 GLU A  84 "
     model   vdw
     1.594 2.450
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.598 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.618 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.647 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.722 1.850
  ... (remaining 28632 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   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.814)
  Mean delta:    0.012 (Z=  0.653)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    7.716 (Z=  4.099)
  Mean delta:    1.706 (Z=  0.911)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -141.39   -38.61  5.00e+00  5.96e+01   7.7*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   154.58    25.42  5.00e+00  2.58e+01   5.1*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   157.32    22.68  5.00e+00  2.06e+01   4.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   158.02    21.98  5.00e+00  1.93e+01   4.4*sigma

  Min. delta:    0.005
  Max. delta:   88.171
  Mean delta:   13.897

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.225
  Mean delta:    0.084

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.054
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="SER A  97  conformer  : HG 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2241  Z= 0.465
    Angle     :  1.612   7.716   4078  Z= 0.693
    Chirality :  0.084   0.225    176
    Planarity :  0.009   0.053    327
    Dihedral  : 12.364  88.171    768
    Min Nonbonded Distance : 1.465
  
  Molprobity Statistics.
    All-atom Clashscore : 12.63
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.11 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  2.42 %
      Favored  : 91.94 %
    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:  0.31 (0.70), residues: 137
    helix:  0.52 (0.52), residues: 72
    sheet:  None (None), residues: 0
    loop : -0.00 (0.88), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.019   0.005   PHE A  15 
   TYR   0.098   0.013   TYR A  89 
   ARG   0.043   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   0.005   PHE A  15 
   TYR   0.079   0.016   TYR A  89 
   ARG   0.006   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  92.70 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     0
  Clashscore            =  12.63
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.61
  MolProbity score      =   2.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.784)
  Mean delta:    0.012 (Z=  0.624)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.908 (Z=  4.224)
  Mean delta:    1.624 (Z=  0.876)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   155.69    24.31  5.00e+00  2.36e+01   4.9*sigma

  Min. delta:    0.018
  Max. delta:   87.054
  Mean delta:   12.169

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.298
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.054
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.444
    Angle     :  1.560   6.908   4079  Z= 0.670
    Chirality :  0.080   0.298    176
    Planarity :  0.009   0.054    327
    Dihedral  : 11.453  87.054    769
    Min Nonbonded Distance : 1.450
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  3.65 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  1.61 %
      Favored  : 98.39 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.05 (0.67), residues: 137
    helix: -0.01 (0.48), residues: 89
    sheet:  None (None), residues: 0
    loop :  0.25 (0.98), residues: 48
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.014   0.003   PHE A  45 
   TYR   0.098   0.014   TYR A  91 
   ARG   0.039   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.008   0.003   PHE A  67 
   TYR   0.078   0.017   TYR A  91 
   ARG   0.006   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A ASP   44": "OD1" <-> "OD2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A TYR  111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   1.46 %
                favored =  94.89 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.56
  MolProbity score      =   1.73

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.964)
  Mean delta:    0.012 (Z=  0.630)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.559 (Z=  4.167)
  Mean delta:    1.566 (Z=  0.840)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   159.94    20.06  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.024
  Max. delta:   89.994
  Mean delta:   11.772

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.182
  Mean delta:    0.074

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.061
  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   2242  Z= 0.449
    Angle     :  1.521   6.559   4079  Z= 0.648
    Chirality :  0.074   0.182    176
    Planarity :  0.008   0.046    327
    Dihedral  : 11.321  89.994    769
    Min Nonbonded Distance : 1.578
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -0.20 (0.68), residues: 137
    helix:  0.38 (0.51), residues: 88
    sheet:  None (None), residues: 0
    loop : -0.92 (0.89), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.024   0.006   PHE A  15 
   TYR   0.074   0.010   TYR A  50 
   ARG   0.049   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.015   0.007   PHE A  15 
   TYR   0.060   0.012   TYR A  50 
   ARG   0.005   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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.

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.52
  MolProbity score      =   1.59

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 463
        1.42 -     1.61: 669
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 139 "
       model="   0" pdb=" OXT HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.231  1.269 -0.038 2.00e-02 2.50e+03 3.56e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.334 -0.013 1.00e-02 1.00e+04 1.82e+00
  bond model="   0" pdb=" C   THR A  82 "
       model="   0" pdb=" N   THR A  83 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.74e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.334 -0.013 1.00e-02 1.00e+04 1.68e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.56e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.72 -   106.75: 59
      106.75 -   112.78: 2698
      112.78 -   118.81: 444
      118.81 -   124.84: 835
      124.84 -   130.86: 43
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
        model="   0" pdb=" C   ILE A  86 "
      ideal   model   delta    sigma   weight residual
     111.00  105.92    5.08 2.80e+00 1.28e-01 3.29e+00
  angle model="   0" pdb=" C   PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  103.67    5.33 3.00e+00 1.11e-01 3.16e+00
  angle model="   0" pdb=" 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  103.85    5.15 3.00e+00 1.11e-01 2.95e+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  113.99   -4.99 3.00e+00 1.11e-01 2.77e+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  105.28    4.72 3.00e+00 1.11e-01 2.48e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.87: 990
       16.87 -    33.75: 24
       33.75 -    50.62: 10
       50.62 -    67.50: 4
       67.50 -    84.37: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  32 "
           model="   0" pdb=" CG  GLU A  32 "
           model="   0" pdb=" CD  GLU A  32 "
           model="   0" pdb=" OE1 GLU A  32 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.49   82.49     1      3.00e+01 1.11e-03 9.27e+00
  dihedral model="   0" pdb=" CA  ASP A  47 "
           model="   0" pdb=" CB  ASP A  47 "
           model="   0" pdb=" CG  ASP A  47 "
           model="   0" pdb=" OD1 ASP A  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -75.58   45.58     1      2.00e+01 2.50e-03 7.20e+00
  dihedral model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
           model="   0" pdb=" CD  GLU A  55 "
           model="   0" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -70.46   70.46     1      3.00e+01 1.11e-03 7.10e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 118
       0.036 -    0.071: 44
       0.071 -    0.106: 9
       0.106 -    0.142: 2
       0.142 -    0.177: 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    2.61   -0.18 2.00e-01 2.50e+01 7.82e-01
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.74e-01
  chirality model="   0" pdb=" CA  VAL A 126 "
            model="   0" pdb=" N   VAL A 126 "
            model="   0" pdb=" C   VAL A 126 "
            model="   0" pdb=" CB  VAL A 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.012 2.00e-02 2.50e+03   5.07e-03 7.72e-01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.003 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 "    0.002 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 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.014 5.00e-02 4.00e+02   2.14e-02 7.33e-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 "   -0.010 2.00e-02 2.50e+03   4.91e-03 7.23e-01
        model="   0" pdb=" CG  TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.29: 309
        2.29 -     2.86: 5162
        2.86 -     3.44: 5387
        3.44 -     4.02: 7387
        4.02 -     4.60: 10805
  Nonbonded interactions: 29050
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  63 "
            model="   0" pdb=" OD2 ASP A  88 "
     model   vdw
     1.708 1.850
  nonbonded model="   0" pdb="HD13 ILE A  78 "
            model="   0" pdb="HD22 LEU A  99 "
     model   vdw
     1.760 2.440
  nonbonded model="   0" pdb=" H   ILE A  86 "
            model="   0" pdb=" O   TYR A  89 "
     model   vdw
     1.790 1.850
  nonbonded model="   0" pdb=" H   ALA A  48 "
            model="   0" pdb="HH11 ARG A 127 "
     model   vdw
     1.807 2.100
  nonbonded model="   0" pdb=" OE1 GLU A  32 "
            model="   0" pdb="HD21 ASN A  72 "
     model   vdw
     1.834 1.850
  ... (remaining 29045 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.701)
  Mean delta:    0.012 (Z=  0.623)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.108 (Z=  4.134)
  Mean delta:    1.647 (Z=  0.887)

                      ----------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   152.59    27.41  5.00e+00  3.00e+01   5.5*sigma
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -154.13   -25.87  5.00e+00  2.68e+01   5.2*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   154.47    25.53  5.00e+00  2.61e+01   5.1*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   157.11    22.89  5.00e+00  2.10e+01   4.6*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   158.99    21.01  5.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.012
  Max. delta:   87.838
  Mean delta:   13.586

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.273
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.058
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.444
    Angle     :  1.570   8.108   4079  Z= 0.676
    Chirality :  0.080   0.273    176
    Planarity :  0.008   0.043    327
    Dihedral  : 11.862  87.838    769
    Min Nonbonded Distance : 1.556
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  7.30 %
      Favored  : 90.51 %
    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: -0.82 (0.69), residues: 137
    helix: -0.08 (0.50), residues: 93
    sheet:  None (None), residues: 0
    loop : -1.35 (0.99), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.069   0.009   TYR A  50 
   ARG   0.047   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.057   0.012   TYR A  50 
   ARG   0.006   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 0.91, per 1000 atoms: 0.41
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.27, 73.238, 46.684, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   2.19 %
                favored =  90.51 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.57
  MolProbity score      =   2.07

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: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.027 (Z=  1.346)
  Mean delta:    0.004 (Z=  0.253)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    5.075 (Z=  1.692)
  Mean delta:    0.589 (Z=  0.299)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   86.372
  Mean delta:   14.057

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.142
  Mean delta:    0.041

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.017
  Mean delta:    0.002

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 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   0.027   2242  Z= 0.181
    Angle     :  1.056   5.075   4079  Z= 0.378
    Chirality :  0.041   0.142    176
    Planarity :  0.002   0.017    327
    Dihedral  : 12.137  86.372    769
    Min Nonbonded Distance : 1.252
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  4.03 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  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: -0.27 (0.72), residues: 137
    helix: -0.05 (0.63), residues: 63
    sheet:  None (None), residues: 0
    loop : -0.17 (0.78), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.004   0.001   PHE A  45 
   TYR   0.014   0.003   TYR A  89 
   ARG   0.004   0.001   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.003   0.001   PHE A  67 
   TYR   0.010   0.003   TYR A  12 
   ARG   0.001   0.000   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0031
  RMS(angles)           =   1.06
  MolProbity score      =   1.77

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  3.234)
  Mean delta:    0.012 (Z=  0.653)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.54     4.06  1.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.214 (Z=  4.057)
  Mean delta:    1.611 (Z=  0.876)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   153.41    26.59  5.00e+00  2.83e+01   5.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   153.50    26.50  5.00e+00  2.81e+01   5.3*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   157.00    23.00  5.00e+00  2.12e+01   4.6*sigma
   A  97  SER  CA
   A  97  SER  C
   A  98  SER  N
   A  98  SER  CA        180.00   158.99    21.01  5.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.009
  Max. delta:   78.416
  Mean delta:   13.686

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.182
  Mean delta:    0.076

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.072
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.465
    Angle     :  1.546   7.214   4079  Z= 0.668
    Chirality :  0.076   0.182    176
    Planarity :  0.009   0.054    327
    Dihedral  : 11.781  78.416    769
    Min Nonbonded Distance : 1.600
  
  Molprobity Statistics.
    All-atom Clashscore : 1.35
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  4.38 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  4.84 %
      Favored  : 91.94 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.06 (0.70), residues: 137
    helix:  0.49 (0.49), residues: 97
    sheet:  None (None), residues: 0
    loop : -1.16 (1.05), residues: 40
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.018   0.004   PHE A  67 
   TYR   0.065   0.009   TYR A  50 
   ARG   0.059   0.014   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.054   0.011   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.183)
  Mean delta:    0.012 (Z=  0.610)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.793 (Z=  4.197)
  Mean delta:    1.546 (Z=  0.850)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.005
  Max. delta:   81.734
  Mean delta:   12.151

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.196
  Mean delta:    0.076

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  36  ASP  CB
   A  36  ASP  CG
   A  36  ASP  OD1
   A  36  ASP  OD2           0.050       0.087       25.25   4.3*sigma

  Min. delta:    0.000
  Max. delta:    0.050
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.434
    Angle     :  1.507   6.793   4079  Z= 0.652
    Chirality :  0.076   0.196    176
    Planarity :  0.008   0.050    327
    Dihedral  : 11.143  81.734    769
    Min Nonbonded Distance : 1.380
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  1.46 %
      Favored  : 97.81 %
    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:  0.16 (0.69), residues: 137
    helix:  0.50 (0.52), residues: 85
    sheet:  None (None), residues: 0
    loop : -0.39 (0.91), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.039   0.008   PHE A  15 
   TYR   0.069   0.009   TYR A  50 
   ARG   0.034   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.024   0.008   PHE A  15 
   TYR   0.057   0.011   TYR A  50 
   ARG   0.004   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.92 %
                favored =  92.70 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   1.35
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.55
  MolProbity score      =   1.71

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.024 (Z=  1.709)
  Mean delta:    0.005 (Z=  0.264)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.863 (Z=  1.520)
  Mean delta:    0.604 (Z=  0.307)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   89.305
  Mean delta:   16.927

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.136
  Mean delta:    0.040

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.008
  Mean delta:    0.002

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.024   2242  Z= 0.189
    Angle     :  1.047   4.864   4079  Z= 0.377
    Chirality :  0.040   0.136    176
    Planarity :  0.002   0.008    327
    Dihedral  : 14.340  89.305    769
    Min Nonbonded Distance : 1.433
  
  Molprobity Statistics.
    All-atom Clashscore : 16.23
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.84 %
      Favored  : 93.43 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  1.61 %
      Favored  : 96.77 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.89 (0.67), residues: 137
    helix: -0.75 (0.53), residues: 71
    sheet:  None (None), residues: 0
    loop : -0.20 (0.79), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 136 
   PHE   0.005   0.002   PHE A  67 
   TYR   0.011   0.002   TYR A  12 
   ARG   0.006   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 136 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.008   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 ===================================


============================== Collecting inputs ==============================

  Ramachandran outliers =   0.73 %
                favored =  97.81 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.51
  MolProbity score      =   1.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.987, 46.135, 57.593, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A ASP   23": "OD1" <-> "OD2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A ASP   47": "OD1" <-> "OD2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A ASP  110": "OD1" <-> "OD2"
    Residue "A ASP  116": "OD1" <-> "OD2"
    Residue "A ASP  118": "OD1" <-> "OD2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   0.73 %
                favored =  93.43 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  16.23
  RMS(bonds)            =   0.0032
  RMS(angles)           =   1.05
  MolProbity score      =   2.30

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  2.179)
  Mean delta:    0.007 (Z=  0.372)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    5.887 (Z=  3.271)
  Mean delta:    0.970 (Z=  0.500)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   87.368
  Mean delta:   12.475

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.164
  Mean delta:    0.051

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.039
  Mean delta:    0.005

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 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      :  0.005   0.022   2242  Z= 0.265
    Angle     :  1.196   5.887   4079  Z= 0.462
    Chirality :  0.051   0.164    176
    Planarity :  0.004   0.030    327
    Dihedral  : 11.262  87.368    769
    Min Nonbonded Distance : 1.533
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    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:  1.26 (0.72), residues: 137
    helix:  0.81 (0.65), residues: 57
    sheet:  1.37 (1.61), residues: 10
    loop :  1.00 (0.82), residues: 70
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.008   0.002   PHE A  67 
   TYR   0.025   0.005   TYR A  91 
   ARG   0.030   0.005   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.005   0.002   PHE A  67 
   TYR   0.020   0.005   TYR A  91 
   ARG   0.003   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.023 (Z=  1.653)
  Mean delta:    0.004 (Z=  0.226)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.970 (Z=  1.507)
  Mean delta:    0.556 (Z=  0.275)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.007
  Max. delta:   88.009
  Mean delta:   13.739

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.158
  Mean delta:    0.040

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.018
  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   2242  Z= 0.161
    Angle     :  1.039   4.970   4079  Z= 0.368
    Chirality :  0.040   0.158    176
    Planarity :  0.002   0.018    327
    Dihedral  : 11.778  88.009    769
    Min Nonbonded Distance : 1.596
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.73 %
      Favored  : 99.27 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.81 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.88 (0.62), residues: 137
    helix: -0.74 (0.58), residues: 69
    sheet:  None (None), residues: 0
    loop : -0.22 (0.62), residues: 68
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.005   0.001   PHE A  67 
   TYR   0.014   0.003   TYR A  89 
   ARG   0.009   0.002   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.010   0.002   TYR A  89 
   ARG   0.002   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 135  HIS

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  99.27 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0028
  RMS(angles)           =   1.04
  MolProbity score      =   1.46

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0048
  RMS(angles)           =   1.20
  MolProbity score      =   1.77

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  3.240)
  Mean delta:    0.012 (Z=  0.628)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.174 (Z=  4.203)
  Mean delta:    1.692 (Z=  0.905)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   138.30    41.70  5.00e+00  6.95e+01   8.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   142.86    37.14  5.00e+00  5.52e+01   7.4*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   147.27    32.73  5.00e+00  4.29e+01   6.5*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   155.42    24.58  5.00e+00  2.42e+01   4.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   156.74    23.26  5.00e+00  2.16e+01   4.7*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   159.45    20.55  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.003
  Max. delta:   85.190
  Mean delta:   13.278

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.192
  Mean delta:    0.079

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.048
  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   2242  Z= 0.447
    Angle     :  1.596   7.174   4079  Z= 0.687
    Chirality :  0.079   0.192    176
    Planarity :  0.009   0.048    327
    Dihedral  : 11.736  85.190    769
    Min Nonbonded Distance : 1.659
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  5.84 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  1.61 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.46 (0.71), residues: 137
    helix:  0.27 (0.51), residues: 86
    sheet:  None (None), residues: 0
    loop : -1.19 (0.98), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.022   0.005   PHE A  67 
   TYR   0.074   0.009   TYR A  50 
   ARG   0.038   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.012   0.005   PHE A  67 
   TYR   0.062   0.010   TYR A  50 
   ARG   0.005   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: 17
        1.23 -     1.42: 446
        1.42 -     1.62: 669
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 2.00e+00
  bond model="   0" pdb=" C   HIS A 136 "
       model="   0" pdb=" N   HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.329  1.309  0.020 1.40e-02 5.10e+03 1.99e+00
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.311  0.018 1.40e-02 5.10e+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  1.312  0.017 1.40e-02 5.10e+03 1.48e+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 1.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.53 -   106.60: 49
      106.60 -   112.68: 2712
      112.68 -   118.75: 441
      118.75 -   124.82: 833
      124.82 -   130.90: 44
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  113.67   -4.67 3.00e+00 1.11e-01 2.43e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.49   -4.49 3.00e+00 1.11e-01 2.24e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.45   -4.45 3.00e+00 1.11e-01 2.20e+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  113.43   -4.43 3.00e+00 1.11e-01 2.19e+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  104.58    4.42 3.00e+00 1.11e-01 2.17e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 984
       17.90 -    35.80: 21
       35.80 -    53.71: 12
       53.71 -    71.61: 7
       71.61 -    89.51: 9
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A  44 "
           model="   0" pdb=" CB  ASP A  44 "
           model="   0" pdb=" CG  ASP A  44 "
           model="   0" pdb=" OD1 ASP A  44 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.34   58.34     1      2.00e+01 2.50e-03 1.14e+01
  dihedral model="   0" pdb=" CA  ASP A  88 "
           model="   0" pdb=" CB  ASP A  88 "
           model="   0" pdb=" CG  ASP A  88 "
           model="   0" pdb=" OD1 ASP A  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.66   57.66     1      2.00e+01 2.50e-03 1.12e+01
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.51   89.51     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 111
       0.029 -    0.058: 48
       0.058 -    0.087: 4
       0.087 -    0.116: 8
       0.116 -    0.145: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.23e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.78e-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    2.57   -0.13 2.00e-01 2.50e+01 4.33e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.014 2.00e-02 2.50e+03   5.22e-03 8.18e-01
        model="   0" pdb=" CG  TYR A 111 "    0.007 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 "    0.001 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 "    0.003 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 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.012 2.00e-02 2.50e+03   5.12e-03 7.87e-01
        model="   0" pdb=" CG  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.000 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 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.001 2.00e-02 2.50e+03   4.55e-03 6.20e-01
        model="   0" pdb=" CG  TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.24: 268
        2.24 -     2.83: 4997
        2.83 -     3.42: 5748
        3.42 -     4.01: 7619
        4.01 -     4.60: 11271
  Nonbonded interactions: 29903
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.656 1.850
  nonbonded model="   0" pdb=" OD1 ASP A 118 "
            model="   0" pdb=" HZ1 LYS A 125 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.736 1.850
  nonbonded model="   0" pdb="HG23 VAL A  41 "
            model="   0" pdb=" H   HIS A  43 "
     model   vdw
     1.740 2.270
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.771 1.850
  ... (remaining 29898 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   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.814)
  Mean delta:    0.012 (Z=  0.653)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.50     4.10  1.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    7.716 (Z=  4.099)
  Mean delta:    1.706 (Z=  0.911)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -141.39   -38.61  5.00e+00  5.96e+01   7.7*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   154.58    25.42  5.00e+00  2.58e+01   5.1*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   157.32    22.68  5.00e+00  2.06e+01   4.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   158.02    21.98  5.00e+00  1.93e+01   4.4*sigma

  Min. delta:    0.005
  Max. delta:   88.171
  Mean delta:   13.897

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.225
  Mean delta:    0.084

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.054
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="SER A  97  conformer  : HG 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2241  Z= 0.465
    Angle     :  1.612   7.716   4078  Z= 0.693
    Chirality :  0.084   0.225    176
    Planarity :  0.009   0.053    327
    Dihedral  : 12.364  88.171    768
    Min Nonbonded Distance : 1.465
  
  Molprobity Statistics.
    All-atom Clashscore : 12.63
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.11 %
      Favored  : 92.70 %
    Rotamer:
      Outliers :  5.65 %
      Allowed  :  2.42 %
      Favored  : 91.94 %
    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:  0.31 (0.70), residues: 137
    helix:  0.52 (0.52), residues: 72
    sheet:  None (None), residues: 0
    loop : -0.00 (0.88), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.019   0.005   PHE A  15 
   TYR   0.098   0.013   TYR A  89 
   ARG   0.043   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   0.005   PHE A  15 
   TYR   0.079   0.016   TYR A  89 
   ARG   0.006   0.002   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   4.38 %
                favored =  89.78 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.60
  MolProbity score      =   2.39

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   2.19 %
                favored =  92.70 %
  Rotamer outliers      =   5.65 %
  C-beta deviations     =     0
  Clashscore            =  12.63
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.61
  MolProbity score      =   2.64

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.024 (Z=  1.491)
  Mean delta:    0.004 (Z=  0.232)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.240 (Z=  1.301)
  Mean delta:    0.683 (Z=  0.324)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   77.761
  Mean delta:   10.507

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.160
  Mean delta:    0.040

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.021
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.024   2242  Z= 0.166
    Angle     :  1.079   5.122   4079  Z= 0.387
    Chirality :  0.040   0.160    176
    Planarity :  0.002   0.021    327
    Dihedral  : 10.480  77.761    769
    Min Nonbonded Distance : 1.089
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  0.73 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.00 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.13 (0.70), residues: 137
    helix:  0.46 (0.63), residues: 63
    sheet:  None (None), residues: 0
    loop :  1.28 (0.74), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.004   0.001   PHE A  15 
   TYR   0.009   0.002   TYR A  68 
   ARG   0.005   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.008   0.002   TYR A 111 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 1.02, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.048, 73.183, 44.975, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.852)
  Mean delta:    0.012 (Z=  0.657)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.38     4.22  1.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    8.875 (Z=  4.219)
  Mean delta:    1.656 (Z=  0.889)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   135.56    44.44  5.00e+00  7.90e+01   8.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   141.60    38.40  5.00e+00  5.90e+01   7.7*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   149.78    30.22  5.00e+00  3.65e+01   6.0*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   153.18    26.82  5.00e+00  2.88e+01   5.4*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00  -159.53   -20.47  5.00e+00  1.68e+01   4.1*sigma

  Min. delta:    0.003
  Max. delta:   85.232
  Mean delta:   13.246

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.231
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.074
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.038   2242  Z= 0.468
    Angle     :  1.581   8.875   4079  Z= 0.679
    Chirality :  0.080   0.231    176
    Planarity :  0.009   0.056    327
    Dihedral  : 11.587  85.232    769
    Min Nonbonded Distance : 1.730
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  :  4.38 %
      Favored  : 89.05 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.84 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.39 (0.69), residues: 137
    helix:  0.28 (0.51), residues: 89
    sheet:  None (None), residues: 0
    loop : -1.15 (0.96), residues: 48
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.015   0.003   PHE A  67 
   TYR   0.073   0.009   TYR A  50 
   ARG   0.060   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.015   0.004   PHE A  67 
   TYR   0.059   0.010   TYR A  50 
   ARG   0.007   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.923)
  Mean delta:    0.012 (Z=  0.644)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    7.689 (Z=  3.957)
  Mean delta:    1.681 (Z=  0.902)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   147.63    32.37  5.00e+00  4.19e+01   6.5*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   151.01    28.99  5.00e+00  3.36e+01   5.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   152.28    27.72  5.00e+00  3.07e+01   5.5*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   154.03    25.97  5.00e+00  2.70e+01   5.2*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   157.27    22.73  5.00e+00  2.07e+01   4.5*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -159.44   -20.56  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.007
  Max. delta:   77.154
  Mean delta:   13.334

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.196
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.084
  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      :  0.009   0.040   2242  Z= 0.459
    Angle     :  1.593   7.689   4079  Z= 0.686
    Chirality :  0.081   0.196    176
    Planarity :  0.009   0.063    327
    Dihedral  : 11.699  77.154    769
    Min Nonbonded Distance : 1.334
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  :  5.84 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  3.23 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.50 (0.69), residues: 137
    helix:  0.65 (0.53), residues: 80
    sheet:  None (None), residues: 0
    loop : -1.80 (0.84), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.003   PHE A  67 
   TYR   0.075   0.010   TYR A 111 
   ARG   0.068   0.014   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.063   0.012   TYR A 111 
   ARG   0.007   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2217
     H or D atoms   : 1105
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.047 (Z=  3.390)
  Mean delta:    0.012 (Z=  0.613)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.47     4.13  1.00e+00  1.71e+01   4.1*sigma
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        121.70   128.92    -7.22  1.80e+00  1.61e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.219 (Z=  4.130)
  Mean delta:    1.592 (Z=  0.872)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   130.31    49.69  5.00e+00  9.88e+01   9.9*sigma

  Min. delta:    0.030
  Max. delta:   86.654
  Mean delta:   13.062

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.204
  Mean delta:    0.077

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A 105  TYR  CB
   A 105  TYR  CG
   A 105  TYR  CD1
   A 105  TYR  CD2
   A 105  TYR  CE1
   A 105  TYR  CE2
   A 105  TYR  CZ
   A 105  TYR  OH            0.055       0.098       60.30   4.9*sigma

  Min. delta:    0.000
  Max. delta:    0.055
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1105
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1105
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="TYR A 105  conformer  : HH 
    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   0.047   2241  Z= 0.437
    Angle     :  1.542   7.219   4078  Z= 0.667
    Chirality :  0.077   0.204    176
    Planarity :  0.008   0.055    327
    Dihedral  : 11.215  86.654    768
    Min Nonbonded Distance : 0.671
  
  Molprobity Statistics.
    All-atom Clashscore : 15.79
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.03 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.11 (0.69), residues: 137
    helix: -0.17 (0.49), residues: 79
    sheet: -2.42 (1.08), residues: 10
    loop :  1.56 (1.03), residues: 48
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.017   0.004   PHE A  45 
   TYR   0.119   0.015   TYR A 105 
   ARG   0.038   0.007   ARG A  58 

  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   0.098   0.017   TYR A 105 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  98.54 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0027
  RMS(angles)           =   1.08
  MolProbity score      =   1.57

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   6.57 %
                favored =  89.05 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.58
  MolProbity score      =   1.92

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   5.84 %
                favored =  88.32 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.59
  MolProbity score      =   2.13

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =  15.79
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.54
  MolProbity score      =   2.24

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.128)
  Mean delta:    0.012 (Z=  0.646)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.42     4.18  1.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.465 (Z=  4.176)
  Mean delta:    1.625 (Z=  0.886)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   158.44    21.56  5.00e+00  1.86e+01   4.3*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   159.58    20.42  5.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.018
  Max. delta:   87.685
  Mean delta:   12.755

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.219
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.080
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.460
    Angle     :  1.555   6.685   4079  Z= 0.674
    Chirality :  0.082   0.219    176
    Planarity :  0.009   0.060    327
    Dihedral  : 11.714  87.685    769
    Min Nonbonded Distance : 1.440
  
  Molprobity Statistics.
    All-atom Clashscore : 14.88
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  5.84 %
      Favored  : 91.97 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  5.65 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.72 (0.67), residues: 137
    helix:  0.07 (0.52), residues: 82
    sheet:  None (None), residues: 0
    loop : -1.22 (0.83), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.017   0.004   PHE A  45 
   TYR   0.066   0.008   TYR A  50 
   ARG   0.065   0.015   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.054   0.010   TYR A  50 
   ARG   0.007   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   2.19 %
                favored =  91.97 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  14.88
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.56
  MolProbity score      =   2.17

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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: 0.98 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.37e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.334 -0.013 1.00e-02 1.00e+04 1.68e+00
  bond model="   0" pdb=" C   GLU A 120 "
       model="   0" pdb=" N   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.49e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.332 -0.011 1.00e-02 1.00e+04 1.27e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.015 1.40e-02 5.10e+03 1.13e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.28 -   106.45: 42
      106.45 -   112.63: 2736
      112.63 -   118.80: 433
      118.80 -   124.98: 826
      124.98 -   131.15: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" C   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     112.10  107.15    4.95 2.50e+00 1.60e-01 3.92e+00
  angle model="   0" pdb=" N   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     110.00  115.04   -5.04 3.00e+00 1.11e-01 2.82e+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  104.33    4.67 3.00e+00 1.11e-01 2.42e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.60   -4.60 3.00e+00 1.11e-01 2.36e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.57   -4.57 3.00e+00 1.11e-01 2.32e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.52: 982
       13.52 -    27.04: 25
       27.04 -    40.56: 18
       40.56 -    54.08: 7
       54.08 -    67.61: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   67.61  -67.61     2      3.00e+01 1.11e-03 4.56e+00
  dihedral model="   0" pdb=" CA  ILE A  51 "
           model="   0" pdb=" C   ILE A  51 "
           model="   0" pdb=" N   PRO A  52 "
           model="   0" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  170.05    9.95     0      5.00e+00 4.00e-02 3.96e+00
  dihedral model="   0" pdb=" CA  ASP A  36 "
           model="   0" pdb=" CB  ASP A  36 "
           model="   0" pdb=" CG  ASP A  36 "
           model="   0" pdb=" OD1 ASP A  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   32.74  -32.74     1      2.00e+01 2.50e-03 3.81e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.029: 122
       0.029 -    0.058: 36
       0.058 -    0.086: 9
       0.086 -    0.115: 5
       0.115 -    0.143: 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    2.58   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.71e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.014 5.00e-02 4.00e+02   2.18e-02 7.60e-01
        model="   0" pdb=" N   PRO A   6 "   -0.038 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  HIS A 139 "    0.008 2.00e-02 2.50e+03   5.05e-03 5.10e-01
        model="   0" pdb=" CG  HIS A 139 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 136 "    0.004 2.00e-02 2.50e+03   4.93e-03 4.86e-01
        model="   0" pdb=" CG  HIS A 136 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 136 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 136 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 136 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 136 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 136 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 136 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 75
        2.11 -     2.74: 4150
        2.74 -     3.36: 6067
        3.36 -     3.98: 7684
        3.98 -     4.60: 11851
  Nonbonded interactions: 29827
  Sorted by model distance:
  nonbonded model="   0" pdb="HD23 LEU A  93 "
            model="   0" pdb=" H   SER A  98 "
     model   vdw
     1.493 2.270
  nonbonded model="   0" pdb="HG22 ILE A  77 "
            model="   0" pdb="HD11 LEU A  93 "
     model   vdw
     1.549 2.440
  nonbonded model="   0" pdb="HD12 LEU A 132 "
            model="   0" pdb=" HD2 HIS A 137 "
     model   vdw
     1.616 2.270
  nonbonded model="   0" pdb=" HB2 LEU A 119 "
            model="   0" pdb=" HD2 ARG A 127 "
     model   vdw
     1.715 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.724 1.850
  ... (remaining 29822 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.045 (Z=  3.200)
  Mean delta:    0.012 (Z=  0.627)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.46     4.14  1.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.004 (Z=  0.002)
  Max. delta:    6.962 (Z=  4.145)
  Mean delta:    1.616 (Z=  0.888)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.048
  Max. delta:   86.651
  Mean delta:   12.720

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.208
  Mean delta:    0.078

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.105       0.179      219.89   8.9*sigma
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.052       0.096       54.13   4.8*sigma
   A  15  PHE  CB
   A  15  PHE  CG
   A  15  PHE  CD1
   A  15  PHE  CD2
   A  15  PHE  CE1
   A  15  PHE  CE2
   A  15  PHE  CZ            0.089       0.092      139.00   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.105
  Mean delta:    0.015

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  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   0.045   2242  Z= 0.447
    Angle     :  1.548   6.962   4079  Z= 0.674
    Chirality :  0.078   0.208    176
    Planarity :  0.012   0.103    327
    Dihedral  : 11.529  86.651    769
    Min Nonbonded Distance : 1.501
  
  Molprobity Statistics.
    All-atom Clashscore : 14.43
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  4.38 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  7.26 %
      Favored  : 91.13 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.16 (0.68), residues: 137
    helix: -0.13 (0.49), residues: 86
    sheet:  None (None), residues: 0
    loop :  0.26 (0.95), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.215   0.027   PHE A  15 
   TYR   0.221   0.021   TYR A  91 
   ARG   0.037   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.141   0.029   PHE A  15 
   TYR   0.179   0.025   TYR A  91 
   ARG   0.005   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Ramachandran outliers =   1.46 %
                favored =  94.16 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  14.43
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.55
  MolProbity score      =   2.22

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.949)
  Mean delta:    0.012 (Z=  0.678)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N         116.20   124.58    -8.38  2.00e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   10.906 (Z=  4.188)
  Mean delta:    1.666 (Z=  0.898)

                      ----------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  -151.88   -28.12  5.00e+00  3.16e+01   5.6*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   157.94    22.06  5.00e+00  1.95e+01   4.4*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -158.92   -21.08  5.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.005
  Max. delta:   89.542
  Mean delta:   13.064

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.273
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.057
  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   2242  Z= 0.483
    Angle     :  1.573  10.906   4079  Z= 0.681
    Chirality :  0.082   0.273    176
    Planarity :  0.008   0.048    327
    Dihedral  : 11.620  89.542    769
    Min Nonbonded Distance : 1.620
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  1.61 %
      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:  0.29 (0.72), residues: 137
    helix:  0.63 (0.53), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.31 (0.95), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 136 
   PHE   0.058   0.010   PHE A  15 
   TYR   0.065   0.009   TYR A  50 
   ARG   0.046   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 136 
   PHE   0.037   0.010   PHE A  15 
   TYR   0.054   0.011   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  2.901)
  Mean delta:    0.012 (Z=  0.606)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.470 (Z=  3.703)
  Mean delta:    1.528 (Z=  0.846)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   159.63    20.37  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.022
  Max. delta:   84.308
  Mean delta:   12.454

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.215
  Mean delta:    0.072

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.068
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.432
    Angle     :  1.493   6.470   4079  Z= 0.648
    Chirality :  0.072   0.215    176
    Planarity :  0.008   0.051    327
    Dihedral  : 10.864  84.308    769
    Min Nonbonded Distance : 1.347
  
  Molprobity Statistics.
    All-atom Clashscore : 17.13
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.81 %
      Favored  : 98.39 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.12 (0.71), residues: 137
    helix:  0.23 (0.53), residues: 83
    sheet: -0.70 (1.58), residues: 10
    loop : -0.24 (1.05), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 139 
   PHE   0.021   0.005   PHE A  67 
   TYR   0.060   0.008   TYR A  50 
   ARG   0.053   0.015   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 139 
   PHE   0.017   0.005   PHE A  67 
   TYR   0.049   0.010   TYR A  50 
   ARG   0.006   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.57
  MolProbity score      =   2.14

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  17.13
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.49
  MolProbity score      =   2.04

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.840)
  Mean delta:    0.012 (Z=  0.622)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.086 (Z=  3.610)
  Mean delta:    1.584 (Z=  0.836)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   152.27    27.73  5.00e+00  3.08e+01   5.5*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   152.75    27.25  5.00e+00  2.97e+01   5.4*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   154.93    25.07  5.00e+00  2.51e+01   5.0*sigma
   A 131  ILE  CA
   A 131  ILE  C
   A 132  LEU  N
   A 132  LEU  CA        180.00   155.01    24.99  5.00e+00  2.50e+01   5.0*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   155.07    24.93  5.00e+00  2.49e+01   5.0*sigma
   A 134  HIS  CA
   A 134  HIS  C
   A 135  HIS  N
   A 135  HIS  CA        180.00   155.79    24.21  5.00e+00  2.34e+01   4.8*sigma
   A 132  LEU  CA
   A 132  LEU  C
   A 133  GLU  N
   A 133  GLU  CA        180.00   155.91    24.09  5.00e+00  2.32e+01   4.8*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   155.97    24.03  5.00e+00  2.31e+01   4.8*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   156.02    23.98  5.00e+00  2.30e+01   4.8*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   159.80    20.20  5.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.009
  Max. delta:   89.148
  Mean delta:   12.792

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.199
  Mean delta:    0.072

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.046
  Mean delta:    0.010

============================= 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   2242  Z= 0.443
    Angle     :  1.532   7.086   4079  Z= 0.648
    Chirality :  0.072   0.199    176
    Planarity :  0.007   0.035    327
    Dihedral  : 11.304  89.148    769
    Min Nonbonded Distance : 1.296
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  :  7.30 %
      Favored  : 86.86 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.00 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.82 (0.69), residues: 137
    helix: -1.04 (0.53), residues: 75
    sheet:  None (None), residues: 0
    loop : -1.29 (0.86), residues: 62
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 134 
   PHE   0.015   0.004   PHE A  67 
   TYR   0.058   0.010   TYR A  50 
   ARG   0.040   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 134 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.048   0.012   TYR A  50 
   ARG   0.003   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (74.621, 59.856, 42.776, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   5.84 %
                favored =  86.86 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.53
  MolProbity score      =   1.94

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  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.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.425)
  Mean delta:    0.012 (Z=  0.628)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.166 (Z=  3.778)
  Mean delta:    1.570 (Z=  0.850)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   159.39    20.61  5.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.000
  Max. delta:   89.964
  Mean delta:   13.558

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.270
  Mean delta:    0.079

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.054
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.447
    Angle     :  1.522   7.166   4079  Z= 0.653
    Chirality :  0.079   0.270    176
    Planarity :  0.009   0.045    327
    Dihedral  : 11.765  89.964    769
    Min Nonbonded Distance : 1.590
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  0.81 %
      Favored  : 95.97 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.29 (0.67), residues: 137
    helix:  0.14 (0.50), residues: 84
    sheet:  None (None), residues: 0
    loop : -0.54 (0.90), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.017   0.005   PHE A  15 
   TYR   0.072   0.009   TYR A  50 
   ARG   0.044   0.011   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.012   0.005   PHE A  67 
   TYR   0.060   0.011   TYR A  50 
   ARG   0.005   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A ASP    7": "OD1" <-> "OD2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 10
        1.23 -     1.42: 454
        1.42 -     1.61: 668
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ARG A 127 "
       model="   0" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.296  0.033 1.40e-02 5.10e+03 5.61e+00
  bond model="   0" pdb=" C   HIS A 134 "
       model="   0" pdb=" N   HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.329  1.300  0.029 1.40e-02 5.10e+03 4.21e+00
  bond model="   0" pdb=" C   ASP A  88 "
       model="   0" pdb=" N   TYR A  89 "
    ideal  model  delta    sigma   weight residual
    1.329  1.357 -0.028 1.40e-02 5.10e+03 3.91e+00
  bond model="   0" pdb=" C   ARG A 129 "
       model="   0" pdb=" N   SER A 130 "
    ideal  model  delta    sigma   weight residual
    1.329  1.302  0.027 1.40e-02 5.10e+03 3.60e+00
  bond model="   0" pdb=" C   ILE A 131 "
       model="   0" pdb=" N   LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.305  0.024 1.40e-02 5.10e+03 2.86e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.81 -   106.08: 42
      106.08 -   112.36: 2696
      112.36 -   118.63: 456
      118.63 -   124.90: 844
      124.90 -   131.17: 41
  Bond angle restraints: 4079
  Sorted by residual:
  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  104.04    4.96 3.00e+00 1.11e-01 2.74e+00
  angle model="   0" pdb=" CD2 HIS A 138 "
        model="   0" pdb=" NE2 HIS A 138 "
        model="   0" pdb=" CE1 HIS A 138 "
      ideal   model   delta    sigma   weight residual
     109.00  107.40    1.60 1.00e+00 1.00e+00 2.55e+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  113.74   -4.74 3.00e+00 1.11e-01 2.50e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.65   -4.65 3.00e+00 1.11e-01 2.41e+00
  angle model="   0" pdb=" CB  PRO A  22 "
        model="   0" pdb=" CA  PRO A  22 "
        model="   0" pdb=" HA  PRO A  22 "
      ideal   model   delta    sigma   weight residual
     109.00  113.49   -4.49 3.00e+00 1.11e-01 2.24e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 984
       17.76 -    35.51: 22
       35.51 -    53.27: 10
       53.27 -    71.03: 6
       71.03 -    88.78: 11
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A 103 "
           model="   0" pdb=" CB  ASP A 103 "
           model="   0" pdb=" CG  ASP A 103 "
           model="   0" pdb=" OD1 ASP A 103 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.17   57.17     1      2.00e+01 2.50e-03 1.10e+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  -88.72   88.72     1      3.00e+01 1.11e-03 1.04e+01
  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   87.44  -87.44     1      3.00e+01 1.11e-03 1.02e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 133
       0.034 -    0.068: 28
       0.068 -    0.103: 8
       0.103 -    0.137: 6
       0.137 -    0.171: 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    2.60   -0.17 2.00e-01 2.50e+01 7.30e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 137 "   -0.010 2.00e-02 2.50e+03   6.14e-03 7.55e-01
        model="   0" pdb=" CG  HIS A 137 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 137 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 137 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 137 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 137 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 137 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 137 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.011 2.00e-02 2.50e+03   4.52e-03 6.14e-01
        model="   0" pdb=" CG  TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.009 2.00e-02 2.50e+03   4.18e-03 5.24e-01
        model="   0" pdb=" CG  TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.11 -     1.80: 11
        1.80 -     2.50: 1709
        2.50 -     3.20: 6719
        3.20 -     3.90: 8107
        3.90 -     4.60: 12485
  Nonbonded interactions: 29031
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.105 1.850
  nonbonded model="   0" pdb="HG21 ILE A 122 "
            model="   0" pdb=" O   LYS A 125 "
     model   vdw
     1.168 2.620
  nonbonded model="   0" pdb=" O   LYS A  10 "
            model="   0" pdb=" HZ3 LYS A  19 "
     model   vdw
     1.540 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ3 LYS A  40 "
     model   vdw
     1.572 1.850
  nonbonded model="   0" pdb=" CG2 ILE A 122 "
            model="   0" pdb=" O   LYS A 125 "
     model   vdw
     1.708 3.100
  ... (remaining 29026 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.52
  MolProbity score      =   1.82

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================


============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.012)
  Mean delta:    0.012 (Z=  0.604)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    5.956 (Z=  3.811)
  Mean delta:    1.552 (Z=  0.850)

                      ----------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   144.51    35.49  5.00e+00  5.04e+01   7.1*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   155.69    24.31  5.00e+00  2.36e+01   4.9*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   159.77    20.23  5.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.010
  Max. delta:   75.556
  Mean delta:   12.665

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.198
  Mean delta:    0.076

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.051
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.430
    Angle     :  1.510   5.956   4079  Z= 0.652
    Chirality :  0.076   0.198    176
    Planarity :  0.008   0.048    327
    Dihedral  : 12.051  84.001    769
    Min Nonbonded Distance : 1.418
  
  Molprobity Statistics.
    All-atom Clashscore : 12.17
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    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: -0.32 (0.68), residues: 137
    helix: -0.10 (0.50), residues: 87
    sheet:  None (None), residues: 0
    loop : -0.13 (0.94), residues: 50
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.024   0.006   PHE A  15 
   TYR   0.063   0.011   TYR A  50 
   ARG   0.044   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.014   0.005   PHE A  15 
   TYR   0.052   0.013   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  12.17
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.51
  MolProbity score      =   1.76

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.862)
  Mean delta:    0.012 (Z=  0.637)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.837 (Z=  3.989)
  Mean delta:    1.635 (Z=  0.895)

                      ----------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   147.80    32.20  5.00e+00  4.15e+01   6.4*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   154.21    25.79  5.00e+00  2.66e+01   5.2*sigma

  Min. delta:    0.031
  Max. delta:   89.193
  Mean delta:   12.692

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.189
  Mean delta:    0.076

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  89  TYR  CB
   A  89  TYR  CG
   A  89  TYR  CD1
   A  89  TYR  CD2
   A  89  TYR  CE1
   A  89  TYR  CE2
   A  89  TYR  CZ
   A  89  TYR  OH            0.050       0.093       50.79   4.6*sigma

  Min. delta:    0.000
  Max. delta:    0.050
  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   2242  Z= 0.454
    Angle     :  1.564   6.837   4079  Z= 0.680
    Chirality :  0.076   0.189    176
    Planarity :  0.009   0.047    327
    Dihedral  : 12.076  89.193    769
    Min Nonbonded Distance : 1.584
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  1.46 %
      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: -0.72 (0.67), residues: 137
    helix: -0.29 (0.49), residues: 86
    sheet:  None (None), residues: 0
    loop : -0.54 (0.91), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.018   0.004   PHE A  45 
   TYR   0.115   0.015   TYR A  89 
   ARG   0.038   0.012   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.010   0.003   PHE A  45 
   TYR   0.093   0.017   TYR A  89 
   ARG   0.004   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Time building chain proxies: 0.91, per 1000 atoms: 0.41
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (77.045, 46.24, 59.534, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.021 (Z=  1.522)
  Mean delta:    0.004 (Z=  0.218)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.332 (Z=  1.726)
  Mean delta:    0.739 (Z=  0.345)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.014
  Max. delta:   82.207
  Mean delta:   10.885

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.139
  Mean delta:    0.040

                       ----------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   0.021   2242  Z= 0.156
    Angle     :  1.085   4.944   4079  Z= 0.391
    Chirality :  0.040   0.139    176
    Planarity :  0.002   0.025    327
    Dihedral  : 10.114  82.207    769
    Min Nonbonded Distance : 1.680
  
  Molprobity Statistics.
    All-atom Clashscore : 7.21
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  1.61 %
      Favored  : 98.39 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  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 (0.72), residues: 137
    helix:  0.52 (0.60), residues: 64
    sheet:  None (None), residues: 0
    loop :  0.51 (0.80), residues: 73
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.009   0.002   PHE A  45 
   TYR   0.010   0.002   TYR A 111 
   ARG   0.006   0.002   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.004   0.001   PHE A  45 
   TYR   0.009   0.002   TYR A 111 
   ARG   0.003   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   2.19 %
                favored =  96.35 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.51
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.56
  MolProbity score      =   1.63

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.21
  RMS(bonds)            =   0.0026
  RMS(angles)           =   1.08
  MolProbity score      =   1.56

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (78.913, 46.038, 64.309, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== 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 GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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:    0.027 (Z=  1.712)
  Mean delta:    0.005 (Z=  0.283)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.849 (Z=  1.673)
  Mean delta:    0.646 (Z=  0.341)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   77.194
  Mean delta:    8.022

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.152
  Mean delta:    0.040

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.017
  Mean delta:    0.002

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 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   0.027   2242  Z= 0.202
    Angle     :  1.033   4.849   4079  Z= 0.381
    Chirality :  0.040   0.152    176
    Planarity :  0.002   0.017    327
    Dihedral  :  8.071  77.194    769
    Min Nonbonded Distance : 1.438
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.05 (0.68), residues: 137
    helix:  0.33 (0.57), residues: 72
    sheet:  None (None), residues: 0
    loop : -0.16 (0.77), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.005   0.002   PHE A  45 
   TYR   0.009   0.002   TYR A  91 
   ARG   0.009   0.002   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.007   0.002   TYR A  91 
   ARG   0.005   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (57.212, 64.767, 60.232, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.021 (Z=  1.509)
  Mean delta:    0.004 (Z=  0.210)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.744 (Z=  1.421)
  Mean delta:    0.711 (Z=  0.344)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.009
  Max. delta:   73.956
  Mean delta:    9.906

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.138
  Mean delta:    0.036

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.023
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.021   2242  Z= 0.150
    Angle     :  1.071   5.128   4079  Z= 0.388
    Chirality :  0.036   0.138    176
    Planarity :  0.002   0.023    327
    Dihedral  :  9.897  80.048    769
    Min Nonbonded Distance : 1.633
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.58 (0.72), residues: 137
    helix: -0.45 (0.56), residues: 73
    sheet:  None (None), residues: 0
    loop :  1.80 (0.85), residues: 64
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.006   0.002   PHE A  15 
   TYR   0.009   0.002   TYR A  81 
   ARG   0.010   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.009   0.002   TYR A  81 
   ARG   0.002   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0034
  RMS(angles)           =   1.03
  MolProbity score      =   1.23

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            =  11.27
  RMS(bonds)            =   0.0025
  RMS(angles)           =   1.07
  MolProbity score      =   1.57

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================

  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.94, 40.093, 73.544, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 8.54e+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 8.02e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.367 -0.038 1.40e-02 5.10e+03 7.42e+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 6.62e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.39e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.46 -   106.10: 103
      106.10 -   111.74: 2467
      111.74 -   117.37: 492
      117.37 -   123.01: 778
      123.01 -   128.65: 239
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.64    3.96 1.00e+00 1.00e+00 1.57e+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  126.53    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
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.57    4.63 1.30e+00 5.92e-01 1.27e+01
  angle model="   0" pdb=" 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  126.69    4.51 1.30e+00 5.92e-01 1.21e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.43: 947
       15.43 -    30.86: 59
       30.86 -    46.29: 19
       46.29 -    61.72: 7
       61.72 -    77.15: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.63   32.37     0      5.00e+00 4.00e-02 4.19e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.01   28.99     0      5.00e+00 4.00e-02 3.36e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.28   27.72     0      5.00e+00 4.00e-02 3.07e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 72
       0.039 -    0.078: 38
       0.078 -    0.118: 36
       0.118 -    0.157: 24
       0.157 -    0.196: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 139 "
            model="   0" pdb=" N   HIS A 139 "
            model="   0" pdb=" C   HIS A 139 "
            model="   0" pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.46e-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    2.32    0.19 2.00e-01 2.50e+01 9.42e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.075 2.00e-02 2.50e+03   3.00e-02 2.70e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.053 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 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.057 2.00e-02 2.50e+03   2.46e-02 1.81e+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 "    0.012 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 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.046 2.00e-02 2.50e+03   1.78e-02 9.53e+00
        model="   0" pdb=" CG  TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.33 -     1.99: 21
        1.99 -     2.64: 2691
        2.64 -     3.29: 6598
        3.29 -     3.95: 7532
        3.95 -     4.60: 11406
  Nonbonded interactions: 28248
  Sorted by model distance:
  nonbonded model="   0" pdb=" OE2 GLU A  49 "
            model="   0" pdb=" HZ3 LYS A 125 "
     model   vdw
     1.334 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.718 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.718 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.818 1.850
  ... (remaining 28243 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)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  2.902)
  Mean delta:    0.012 (Z=  0.631)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.54     4.06  1.00e+00  1.65e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.036 (Z=  4.063)
  Mean delta:    1.677 (Z=  0.901)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  95  ASP  CA
   A  95  ASP  C
   A  96  GLY  N
   A  96  GLY  CA        180.00  -149.19   -30.81  5.00e+00  3.80e+01   6.2*sigma
   A 129  ARG  CA
   A 129  ARG  C
   A 130  SER  N
   A 130  SER  CA        180.00   153.29    26.71  5.00e+00  2.85e+01   5.3*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   154.86    25.14  5.00e+00  2.53e+01   5.0*sigma
   A  86  ILE  CA
   A  86  ILE  C
   A  87  GLY  N
   A  87  GLY  CA        180.00  -154.96   -25.04  5.00e+00  2.51e+01   5.0*sigma

  Min. delta:    0.009
  Max. delta:   84.339
  Mean delta:   13.309

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.232
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.064
  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   2242  Z= 0.449
    Angle     :  1.579   7.036   4079  Z= 0.682
    Chirality :  0.080   0.232    176
    Planarity :  0.008   0.048    327
    Dihedral  : 11.781  84.339    769
    Min Nonbonded Distance : 1.346
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  5.11 %
      Allowed  :  8.76 %
      Favored  : 86.13 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  3.23 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.40 (0.66), residues: 137
    helix: -0.21 (0.52), residues: 74
    sheet:  None (None), residues: 0
    loop : -1.79 (0.78), residues: 63
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 137 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.071   0.010   TYR A  50 
   ARG   0.050   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 137 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.060   0.011   TYR A  50 
   ARG   0.006   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   5.11 %
                favored =  86.13 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.58
  MolProbity score      =   2.59

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 ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.847)
  Mean delta:    0.012 (Z=  0.636)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.44     4.16  1.00e+00  1.73e+01   4.2*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.749 (Z=  4.162)
  Mean delta:    1.600 (Z=  0.884)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00  -154.66   -25.34  5.00e+00  2.57e+01   5.1*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00  -155.74   -24.26  5.00e+00  2.35e+01   4.9*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   155.76    24.24  5.00e+00  2.35e+01   4.8*sigma
   A 117  PRO  CA
   A 117  PRO  C
   A 118  ASP  N
   A 118  ASP  CA        180.00  -158.25   -21.75  5.00e+00  1.89e+01   4.3*sigma

  Min. delta:    0.007
  Max. delta:   86.597
  Mean delta:   13.529

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.198
  Mean delta:    0.078

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.047       0.085       44.66   4.2*sigma

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.453
    Angle     :  1.548   6.749   4079  Z= 0.674
    Chirality :  0.078   0.198    176
    Planarity :  0.008   0.045    327
    Dihedral  : 11.562  86.597    769
    Min Nonbonded Distance : 1.587
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  5.65 %
      Favored  : 91.13 %
    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: -0.03 (0.48), residues: 94
    sheet:  None (None), residues: 0
    loop :  1.56 (1.00), residues: 43
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.021   0.004   PHE A  45 
   TYR   0.107   0.013   TYR A  91 
   ARG   0.031   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.012   0.003   PHE A  45 
   TYR   0.085   0.015   TYR A  91 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.55
  MolProbity score      =   1.89

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (50.721, 52.091, 62.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.884)
  Mean delta:    0.012 (Z=  0.631)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.816 (Z=  3.955)
  Mean delta:    1.596 (Z=  0.865)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   158.10    21.90  5.00e+00  1.92e+01   4.4*sigma

  Min. delta:    0.001
  Max. delta:   88.883
  Mean delta:   13.086

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.236
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.064
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.450
    Angle     :  1.540   7.816   4079  Z= 0.663
    Chirality :  0.080   0.236    176
    Planarity :  0.009   0.060    327
    Dihedral  : 11.528  88.883    769
    Min Nonbonded Distance : 1.594
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.40 (0.66), residues: 137
    helix:  0.17 (0.50), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.77 (0.85), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.025   0.005   PHE A  15 
   TYR   0.139   0.014   TYR A  81 
   ARG   0.051   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.016   0.006   PHE A  15 
   TYR   0.113   0.017   TYR A  81 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (59.807, 35.635, 71.719, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.042 (Z=  2.832)
  Mean delta:    0.012 (Z=  0.628)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.375 (Z=  3.729)
  Mean delta:    1.617 (Z=  0.883)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   152.95    27.05  5.00e+00  2.93e+01   5.4*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   156.84    23.16  5.00e+00  2.15e+01   4.6*sigma

  Min. delta:    0.017
  Max. delta:   88.800
  Mean delta:   12.952

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.193
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.069
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.042   2242  Z= 0.447
    Angle     :  1.557   6.375   4079  Z= 0.674
    Chirality :  0.080   0.193    176
    Planarity :  0.008   0.051    327
    Dihedral  : 11.648  88.800    769
    Min Nonbonded Distance : 1.303
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  4.38 %
      Favored  : 93.43 %
    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: -0.46 (0.67), residues: 137
    helix: -0.33 (0.48), residues: 84
    sheet:  None (None), residues: 0
    loop :  0.04 (0.94), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.030   0.007   PHE A  15 
   TYR   0.066   0.011   TYR A 111 
   ARG   0.055   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.020   0.007   PHE A  15 
   TYR   0.055   0.013   TYR A  50 
   ARG   0.007   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  94.16 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.54
  MolProbity score      =   2.10

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   2.19 %
                favored =  93.43 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.56
  MolProbity score      =   2.00

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.19 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: 0.68
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.81 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 56
        1.23 -     1.42: 416
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.85e+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 6.12e+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 5.94e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.90e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.62e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.26 -   105.96: 83
      105.96 -   111.66: 2450
      111.66 -   117.36: 526
      117.36 -   123.06: 788
      123.06 -   128.76: 232
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.58    4.02 1.00e+00 1.00e+00 1.62e+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  118.82    3.78 1.00e+00 1.00e+00 1.43e+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  118.83    3.77 1.00e+00 1.00e+00 1.42e+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  116.24   -3.64 1.00e+00 1.00e+00 1.32e+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
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.13: 952
       15.13 -    30.25: 57
       30.25 -    45.38: 19
       45.38 -    60.51: 3
       60.51 -    75.64: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.34   19.66     0      5.00e+00 4.00e-02 1.55e+01
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.27   17.73     0      5.00e+00 4.00e-02 1.26e+01
  dihedral model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" CB  THR A  82 "
           model="   0" pdb=" OG1 THR A  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    0.89   59.11     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 81
       0.044 -    0.087: 44
       0.087 -    0.131: 38
       0.131 -    0.174: 11
       0.174 -    0.217: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.18e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.86e-01
  chirality model="   0" pdb=" CG  LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
            model="   0" pdb=" CD1 LEU A  93 "
            model="   0" pdb=" CD2 LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.29e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.070 2.00e-02 2.50e+03   3.06e-02 2.81e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 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 "   -0.010 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 "    0.062 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 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.016 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.066 2.00e-02 2.50e+03   2.61e-02 2.04e+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 "    0.015 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 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.045 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.019 2.00e-02 2.50e+03   3.79e-02 1.44e+01
        model="   0" pdb=" CG  ASP A  36 "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 189
        2.23 -     2.82: 4564
        2.82 -     3.41: 5871
        3.41 -     4.01: 7357
        4.01 -     4.60: 10834
  Nonbonded interactions: 28815
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.635 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.671 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.705 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.708 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.758 1.850
  ... (remaining 28810 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: 76
        1.23 -     1.43: 396
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 8.74e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.33e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.72e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.60e+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 5.53e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.30 -   106.03: 106
      106.03 -   111.76: 2466
      111.76 -   117.49: 497
      117.49 -   123.23: 813
      123.23 -   128.96: 197
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.41    4.19 1.00e+00 1.00e+00 1.76e+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
  angle model="   0" pdb=" N   LEU A  93 "
        model="   0" pdb=" CA  LEU A  93 "
        model="   0" pdb=" C   LEU A  93 "
      ideal   model   delta    sigma   weight residual
     111.00  101.52    9.48 2.80e+00 1.28e-01 1.15e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.95   -3.35 1.00e+00 1.00e+00 1.12e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.26    3.34 1.00e+00 1.00e+00 1.12e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.66: 952
       16.66 -    33.32: 62
       33.32 -    49.99: 11
       49.99 -    66.65: 6
       66.65 -    83.31: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.99   38.01     0      5.00e+00 4.00e-02 5.78e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.39   35.61     0      5.00e+00 4.00e-02 5.07e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.11   34.89     0      5.00e+00 4.00e-02 4.87e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 74
       0.049 -    0.098: 65
       0.098 -    0.147: 30
       0.147 -    0.196: 4
       0.196 -    0.244: 3
  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    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.064 2.00e-02 2.50e+03   2.77e-02 2.31e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 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   2.10e-02 1.33e+01
        model="   0" pdb=" CG  TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 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 "    0.013 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 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.047 2.00e-02 2.50e+03   1.83e-02 1.00e+01
        model="   0" pdb=" CG  TYR A  12 "    0.013 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 "    0.004 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 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 398
        2.32 -     2.89: 5198
        2.89 -     3.46: 5270
        3.46 -     4.03: 6725
        4.03 -     4.60: 10091
  Nonbonded interactions: 27682
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.753 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.763 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.765 1.850
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" HE2 TYR A  81 "
     model   vdw
     1.797 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.834 1.850
  ... (remaining 27677 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.93 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.884)
  Mean delta:    0.012 (Z=  0.631)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.816 (Z=  3.955)
  Mean delta:    1.596 (Z=  0.865)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   158.10    21.90  5.00e+00  1.92e+01   4.4*sigma

  Min. delta:    0.001
  Max. delta:   88.883
  Mean delta:   13.086

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.236
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.064
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.450
    Angle     :  1.540   7.816   4079  Z= 0.663
    Chirality :  0.080   0.236    176
    Planarity :  0.009   0.060    327
    Dihedral  : 11.528  88.883    769
    Min Nonbonded Distance : 1.594
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.40 (0.66), residues: 137
    helix:  0.17 (0.50), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.77 (0.85), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.025   0.005   PHE A  15 
   TYR   0.139   0.014   TYR A  81 
   ARG   0.051   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.016   0.006   PHE A  15 
   TYR   0.113   0.017   TYR A  81 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 88
        1.23 -     1.43: 384
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.22e+00
  bond model="   0" pdb=" 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 6.05e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.51e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.25e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.301  0.029 1.30e-02 5.92e+03 5.11e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.07 -   105.83: 67
      105.83 -   111.60: 2453
      111.60 -   117.36: 538
      117.36 -   123.12: 805
      123.12 -   128.89: 216
  Bond angle restraints: 4079
  Sorted by residual:
  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  126.63    4.57 1.30e+00 5.92e-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  126.70    4.50 1.30e+00 5.92e-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  116.06   -3.46 1.00e+00 1.00e+00 1.20e+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  119.33    3.27 1.00e+00 1.00e+00 1.07e+01
  angle model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     121.70  127.50   -5.80 1.80e+00 3.09e-01 1.04e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 962
       16.74 -    33.47: 44
       33.47 -    50.21: 16
       50.21 -    66.95: 9
       66.95 -    83.68: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.64   17.36     0      5.00e+00 4.00e-02 1.21e+01
  dihedral model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
           model="   0" pdb=" CB  HIS A 139 "
           model="   0" pdb=" CG  HIS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.58  -57.42     3      1.50e+01 4.44e-03 9.44e+00
  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
     -60.00 -116.59   56.59     3      1.50e+01 4.44e-03 9.41e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 70
       0.038 -    0.075: 46
       0.075 -    0.113: 34
       0.113 -    0.150: 22
       0.150 -    0.188: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.83e-01
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.28e-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    2.34    0.17 2.00e-01 2.50e+01 6.91e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.077 2.00e-02 2.50e+03   3.45e-02 3.57e+01
        model="   0" pdb=" CG  TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.068 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.067 2.00e-02 2.50e+03   2.93e-02 2.58e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.023 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 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.060 2.00e-02 2.50e+03   2.40e-02 1.73e+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 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.63 -     2.23: 210
        2.23 -     2.82: 4599
        2.82 -     3.41: 5937
        3.41 -     4.01: 7378
        4.01 -     4.60: 11022
  Nonbonded interactions: 29146
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.633 1.850
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.672 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.720 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.767 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.800 1.850
  ... (remaining 29141 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.73 %
                favored =  94.16 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.54
  MolProbity score      =   2.10

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 0.96, per 1000 atoms: 0.43
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (44.5, 74.988, 60.943, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 69
        1.23 -     1.43: 403
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 7.83e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.57e+00
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.404 -0.030 1.10e-02 8.26e+03 7.34e+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 7.26e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.18e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.38 -   106.33: 133
      106.33 -   112.28: 2545
      112.28 -   118.23: 444
      118.23 -   124.17: 861
      124.17 -   130.12: 96
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  130.12   -8.42 1.80e+00 3.09e-01 2.19e+01
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.41    4.19 1.00e+00 1.00e+00 1.76e+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  125.79    5.41 1.30e+00 5.92e-01 1.73e+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  128.99   -7.29 1.80e+00 3.09e-01 1.64e+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 1.45e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 963
       17.98 -    35.97: 49
       35.97 -    53.95: 11
       53.95 -    71.93: 8
       71.93 -    89.91: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.82   30.18     0      5.00e+00 4.00e-02 3.64e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.66   28.34     0      5.00e+00 4.00e-02 3.21e+01
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.97  -27.03     0      5.00e+00 4.00e-02 2.92e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 79
       0.050 -    0.100: 54
       0.100 -    0.149: 34
       0.149 -    0.199: 5
      
  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
 0.199 -    0.249: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality model="   0" pdb=" CA  TYR A  81 "
            model="   0" pdb=" N   TYR A  81 "
            model="   0" pdb=" C   TYR A  81 "
            model="   0" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.052 2.00e-02 2.50e+03   2.18e-02 1.42e+01
        model="   0" pdb=" CG  TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.011 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 "    0.055 2.00e-02 2.50e+03   2.15e-02 1.38e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 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 "   -0.020 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 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  67 "    0.041 2.00e-02 2.50e+03   1.76e-02 9.29e+00
        model="   0" pdb=" CG  PHE A  67 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  67 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  67 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  67 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  67 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  67 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  67 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  67 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  67 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  67 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  67 "    0.027 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 205
        2.23 -     2.83: 4627
        2.83 -     3.42: 5735
        3.42 -     4.01: 6857
        4.01 -     4.60: 10408
  Nonbonded interactions: 27832
  Sorted by model distance:
  nonbonded model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" HB3 SER A  97 "
     model   vdw
     1.642 2.770
  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=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.738 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.751 1.850
  nonbonded model="   0" pdb="HD11 LEU A  93 "
            model="   0" pdb="HE21 GLN A 100 "
     model   vdw
     1.772 2.270
  ... (remaining 27827 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.549, 49.659, 85.138, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.973, 58.937, 40.241, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 0.98, per 1000 atoms: 0.44
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.516, 80.836, 44.874, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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=  1.888)
  Mean delta:    0.005 (Z=  0.301)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    5.076 (Z=  1.813)
  Mean delta:    0.777 (Z=  0.365)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.008
  Max. delta:   84.374
  Mean delta:   11.296

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.177
  Mean delta:    0.045

                       ----------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      :  0.004   0.038   2242  Z= 0.214
    Angle     :  1.099   5.334   4079  Z= 0.399
    Chirality :  0.045   0.177    176
    Planarity :  0.003   0.021    327
    Dihedral  : 10.986  84.374    769
    Min Nonbonded Distance : 1.708
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.02 (0.69), residues: 137
    helix: -0.07 (0.59), residues: 71
    sheet:  None (None), residues: 0
    loop :  0.33 (0.76), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.008   0.002   PHE A  15 
   TYR   0.012   0.003   TYR A  50 
   ARG   0.008   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.006   0.002   PHE A  15 
   TYR   0.009   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 ===================================

  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (43.524, 64.659, 65.88, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================

  Time building chain proxies: 0.59, per 1000 atoms: 0.27
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.205, 58.535, 74.088, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.16 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0037
  RMS(angles)           =   1.10
  MolProbity score      =   1.36

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (45.306, 73.541, 48.285, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 100
        1.23 -     1.43: 372
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 8.49e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.19e+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 8.18e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.42e+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 7.02e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.82 -   106.44: 126
      106.44 -   112.05: 2513
      112.05 -   117.67: 439
      117.67 -   123.28: 816
      123.28 -   128.90: 185
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.53    4.07 1.00e+00 1.00e+00 1.65e+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  126.20    5.00 1.30e+00 5.92e-01 1.48e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  118.80    3.80 1.00e+00 1.00e+00 1.44e+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  126.41    4.79 1.30e+00 5.92e-01 1.36e+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  126.66    4.54 1.30e+00 5.92e-01 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 969
       17.51 -    35.03: 46
       35.03 -    52.54: 14
       52.54 -    70.05: 3
       70.05 -    87.56: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.29   20.71     0      5.00e+00 4.00e-02 1.72e+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  164.80   15.20     0      5.00e+00 4.00e-02 9.24e+00
  dihedral model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" CB  HIS A 137 "
           model="   0" pdb=" CG  HIS A 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -128.03  -51.97     3      1.50e+01 4.44e-03 9.07e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.041: 80
       0.041 -    0.081: 39
       0.081 -    0.122: 36
       0.122 -    0.162: 19
       0.162 -    0.202: 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 1.02e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.25e-01
  chirality model="   0" pdb=" CG  LEU A  39 "
            model="   0" pdb=" CB  LEU A  39 "
            model="   0" pdb=" CD1 LEU A  39 "
            model="   0" pdb=" CD2 LEU A  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.17e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.081 2.00e-02 2.50e+03   3.61e-02 3.91e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.016 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 "    0.013 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 "   -0.074 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.024 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.048 2.00e-02 2.50e+03   1.86e-02 1.04e+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 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.028 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 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.007 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   1.84e-02 1.02e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.012 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 "    0.003 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 "   -0.027 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 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.001 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 143
        2.19 -     2.79: 4314
        2.79 -     3.39: 6079
        3.39 -     4.00: 7459
        4.00 -     4.60: 11217
  Nonbonded interactions: 29212
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.581 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.675 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.748 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.751 1.850
  ... (remaining 29207 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.789, 78.683, 47.198, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 1
        1.23 -     1.42: 464
        1.42 -     1.61: 667
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 137 "
       model="   0" pdb=" N   HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.329  1.303  0.026 1.40e-02 5.10e+03 3.38e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.18e+00
  bond model="   0" pdb=" C   THR A  82 "
       model="   0" pdb=" N   THR A  83 "
    ideal  model  delta    sigma   weight residual
    1.329  1.349 -0.020 1.40e-02 5.10e+03 2.07e+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 1.77e+00
  bond model="   0" pdb=" C   GLU A  75 "
       model="   0" pdb=" N   SER A  76 "
    ideal  model  delta    sigma   weight residual
    1.329  1.347 -0.018 1.40e-02 5.10e+03 1.59e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.64 -   106.72: 55
      106.72 -   112.79: 2706
      112.79 -   118.87: 442
      118.87 -   124.95: 834
      124.95 -   131.02: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.21   -5.21 3.00e+00 1.11e-01 3.01e+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  103.98    5.02 3.00e+00 1.11e-01 2.80e+00
  angle model="   0" pdb=" C   PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  104.10    4.90 3.00e+00 1.11e-01 2.67e+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  104.15    4.85 3.00e+00 1.11e-01 2.61e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.58   -4.58 3.00e+00 1.11e-01 2.33e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.27: 979
       17.27 -    34.54: 33
       34.54 -    51.81: 12
       51.81 -    69.08: 3
       69.08 -    86.35: 6
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.35   86.35     1      3.00e+01 1.11e-03 9.99e+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  -78.16   78.16     1      3.00e+01 1.11e-03 8.48e+00
  dihedral model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
           model="   0" pdb=" CD  GLU A  55 "
           model="   0" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   73.00  -73.00     1      3.00e+01 1.11e-03 7.55e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 108
       0.027 -    0.054: 47
       0.054 -    0.081: 10
       0.081 -    0.108: 7
       0.108 -    0.135: 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    2.57   -0.14 2.00e-01 2.50e+01 4.58e-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   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.64e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.019 2.00e-02 2.50e+03   7.31e-03 1.60e+00
        model="   0" pdb=" CG  TYR A  91 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.015 5.00e-02 4.00e+02   2.27e-02 8.23e-01
        model="   0" pdb=" N   PRO A   6 "   -0.039 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.012 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.013 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.007 2.00e-02 2.50e+03   4.35e-03 5.68e-01
        model="   0" pdb=" CG  TYR A  81 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 164
        2.20 -     2.80: 4591
        2.80 -     3.40: 5842
        3.40 -     4.00: 7410
        4.00 -     4.60: 11191
  Nonbonded interactions: 29198
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 LEU A  70 "
            model="   0" pdb="HD11 ILE A  78 "
     model   vdw
     1.599 2.440
  nonbonded model="   0" pdb="HG21 ILE A  78 "
            model="   0" pdb=" HB2 LEU A  99 "
     model   vdw
     1.675 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.689 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.716 1.850
  nonbonded model="   0" pdb=" O   LYS A  79 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.754 1.850
  ... (remaining 29193 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== Collecting inputs ==============================

  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (53.909, 68.397, 52.743, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.10, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.217, 59.512, 75.508, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A PHE   15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.09, per 1000 atoms: 0.49
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (51.088, 73.223, 47.811, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  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.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 87
        1.23 -     1.43: 385
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   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 6.93e+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 6.29e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.80e+00
  bond model="   0" pdb=" CZ  ARG A 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 5.62e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.42e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   106.17: 103
      106.17 -   111.80: 2484
      111.80 -   117.43: 481
      117.43 -   123.06: 783
      123.06 -   128.69: 228
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.75   -4.15 1.00e+00 1.00e+00 1.72e+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  118.61    3.99 1.00e+00 1.00e+00 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  126.29    4.91 1.30e+00 5.92e-01 1.43e+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 1.33e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.10   -3.50 1.00e+00 1.00e+00 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.47: 926
       13.47 -    26.95: 74
       26.95 -    40.42: 20
       40.42 -    53.90: 8
       53.90 -    67.37: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.39  -23.61     0      5.00e+00 4.00e-02 2.23e+01
  dihedral model="   0" pdb=" N   ASP A  95 "
           model="   0" pdb=" CA  ASP A  95 "
           model="   0" pdb=" CB  ASP A  95 "
           model="   0" pdb=" CG  ASP A  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.28  -59.72     3      1.50e+01 4.44e-03 9.48e+00
  dihedral model="   0" pdb=" N   HIS A 134 "
           model="   0" pdb=" CA  HIS A 134 "
           model="   0" pdb=" CB  HIS A 134 "
           model="   0" pdb=" CG  HIS A 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.19  -58.81     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 74
       0.042 -    0.084: 48
       0.084 -    0.126: 36
       0.126 -    0.168: 14
       0.168 -    0.210: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.59e-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 7.87e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.209 2.00e-02 2.50e+03   8.33e-02 2.08e+02
        model="   0" pdb=" CG  TYR A  81 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.044 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.144 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.063 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.077 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.025 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.124 2.00e-02 2.50e+03   5.20e-02 8.10e+01
        model="   0" pdb=" CG  TYR A  89 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.098 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "   -0.119 2.00e-02 2.50e+03   4.87e-02 7.11e+01
        model="   0" pdb=" CG  PHE A  15 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "    0.065 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "   -0.070 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.44 -     2.07: 69
        2.07 -     2.70: 3511
        2.70 -     3.34: 6394
        3.34 -     3.97: 7673
        3.97 -     4.60: 11671
  Nonbonded interactions: 29318
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   THR A  82 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     1.438 2.620
  nonbonded model="   0" pdb=" HD2 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.473 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.593 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.596 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.704 1.850
  ... (remaining 29313 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


============================== 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: 1.15 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: 1.04
  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.

  Time building chain proxies: 0.85, per 1000 atoms: 0.38
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (64.105, 42.09, 80.558, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 113
        1.23 -     1.43: 359
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.31e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.16e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.25e+00
  bond model="   0" pdb=" CE1 HIS A 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 6.22e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.77e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.25 -   106.79: 156
      106.79 -   112.33: 2529
      112.33 -   117.87: 404
      117.87 -   123.41: 825
      123.41 -   128.95: 165
  Bond angle restraints: 4079
  Sorted by residual:
  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  117.96   -5.36 1.00e+00 1.00e+00 2.87e+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  118.51    4.09 1.00e+00 1.00e+00 1.67e+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  118.94    3.66 1.00e+00 1.00e+00 1.34e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.64    4.56 1.30e+00 5.92e-01 1.23e+01
  angle model="   0" pdb=" 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  126.94    4.26 1.30e+00 5.92e-01 1.07e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.81: 967
       16.81 -    33.61: 44
       33.61 -    50.42: 18
       50.42 -    67.23: 2
       67.23 -    84.04: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A  74 "
           model="   0" pdb=" C   ASP A  74 "
           model="   0" pdb=" N   GLU A  75 "
           model="   0" pdb=" CA  GLU A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+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 -162.43  -17.57     0      5.00e+00 4.00e-02 1.24e+01
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -165.70  -14.30     0      5.00e+00 4.00e-02 8.18e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.045: 76
       0.045 -    0.089: 45
       0.089 -    0.134: 39
       0.134 -    0.178: 13
       0.178 -    0.222: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality model="   0" pdb=" CA  ASP A  74 "
            model="   0" pdb=" N   ASP A  74 "
            model="   0" pdb=" C   ASP A  74 "
            model="   0" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality model="   0" pdb=" CA  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
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.081 2.00e-02 2.50e+03   3.18e-02 3.04e+01
        model="   0" pdb=" CG  TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.002 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   2.62e-02 2.06e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.023 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 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.056 2.00e-02 2.50e+03   2.31e-02 1.60e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.044 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 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 96
        2.12 -     2.74: 3858
        2.74 -     3.36: 6385
        3.36 -     3.98: 7851
        3.98 -     4.60: 11691
  Nonbonded interactions: 29881
  Sorted by model distance:
  nonbonded model="   0" pdb="HG12 ILE A  77 "
            model="   0" pdb="HD22 LEU A  93 "
     model   vdw
     1.495 2.440
  nonbonded model="   0" pdb=" O   GLY A  80 "
            model="   0" pdb=" O   LEU A  93 "
     model   vdw
     1.567 2.800
  nonbonded model="   0" pdb=" HD1 TYR A  91 "
            model="   0" pdb="HD23 LEU A  99 "
     model   vdw
     1.583 2.270
  nonbonded model="   0" pdb=" HA  TYR A  81 "
            model="   0" pdb=" O   LEU A  93 "
     model   vdw
     1.601 2.620
  nonbonded model="   0" pdb="HE22 GLN A  66 "
            model="   0" pdb="HD12 ILE A  86 "
     model   vdw
     1.707 2.270
  ... (remaining 29876 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 67
        1.23 -     1.43: 405
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" N   PRO A 117 "
       model="   0" pdb=" CD  PRO A 117 "
    ideal  model  delta    sigma   weight residual
    1.473  1.430  0.043 1.40e-02 5.10e+03 9.42e+00
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.370 -0.041 1.40e-02 5.10e+03 8.66e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.41e+00
  bond model="   0" pdb=" C   ALA A 124 "
       model="   0" pdb=" N   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.329  1.367 -0.038 1.40e-02 5.10e+03 7.21e+00
  bond model="   0" pdb=" C   PRO A 117 "
       model="   0" pdb=" N   ASP A 118 "
    ideal  model  delta    sigma   weight residual
    1.329  1.366 -0.037 1.40e-02 5.10e+03 7.10e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.03 -   106.19: 103
      106.19 -   112.35: 2578
      112.35 -   118.50: 477
      118.50 -   124.66: 847
      124.66 -   130.81: 74
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  130.81   -9.11 1.80e+00 3.09e-01 2.56e+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  118.57    4.03 1.00e+00 1.00e+00 1.62e+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  116.35   -3.75 1.00e+00 1.00e+00 1.41e+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  126.40    4.80 1.30e+00 5.92e-01 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  126.52    4.68 1.30e+00 5.92e-01 1.30e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.70: 966
       17.70 -    35.41: 43
       35.41 -    53.11: 19
       53.11 -    70.81: 4
       70.81 -    88.52: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.38  -45.62     0      5.00e+00 4.00e-02 8.33e+01
  dihedral model="   0" pdb=" CA  ASP A 118 "
           model="   0" pdb=" C   ASP A 118 "
           model="   0" pdb=" N   LEU A 119 "
           model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.34   23.66     0      5.00e+00 4.00e-02 2.24e+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  160.36   19.64     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.049: 86
       0.049 -    0.097: 51
       0.097 -    0.145: 32
       0.145 -    0.193: 6
       0.193 -    0.241: 1
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.87e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.81e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.070 2.00e-02 2.50e+03   3.06e-02 2.81e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.062 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.058 2.00e-02 2.50e+03   2.27e-02 1.55e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 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 "    0.015 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 "    0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.048 2.00e-02 2.50e+03   1.85e-02 1.02e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.028 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 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 215
        2.24 -     2.83: 4746
        2.83 -     3.42: 5790
        3.42 -     4.01: 7391
        4.01 -     4.60: 10899
  Nonbonded interactions: 29041
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ASP A 118 "
            model="   0" pdb=" H   ILE A 122 "
     model   vdw
     1.654 1.850
  nonbonded model="   0" pdb=" HG1 THR A  82 "
            model="   0" pdb=" O   ASP A  88 "
     model   vdw
     1.679 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.729 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.740 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.749 1.850
  ... (remaining 29036 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.13 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (84.005, 45.639, 45.147, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.08 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  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.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 38
        1.23 -     1.42: 434
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 6.64e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.55e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.54e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 5.93e+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 5.83e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.28 -   105.97: 83
      105.97 -   111.65: 2450
      111.65 -   117.33: 514
      117.33 -   123.02: 803
      123.02 -   128.70: 229
  Bond angle restraints: 4079
  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  119.03    3.57 1.00e+00 1.00e+00 1.28e+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  116.03   -3.43 1.00e+00 1.00e+00 1.18e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.75    4.45 1.30e+00 5.92e-01 1.17e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.76    4.44 1.30e+00 5.92e-01 1.17e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.51: 965
       16.51 -    33.02: 44
       33.02 -    49.53: 17
       49.53 -    66.05: 4
       66.05 -    82.56: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.71   31.29     0      5.00e+00 4.00e-02 3.92e+01
  dihedral model="   0" pdb=" CA  SER A  98 "
           model="   0" pdb=" C   SER A  98 "
           model="   0" pdb=" N   LEU A  99 "
           model="   0" pdb=" CA  LEU A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.45   19.55     0      5.00e+00 4.00e-02 1.53e+01
  dihedral model="   0" pdb=" N   MET A 128 "
           model="   0" pdb=" CA  MET A 128 "
           model="   0" pdb=" CB  MET A 128 "
           model="   0" pdb=" CG  MET A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.11   59.11     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.038: 74
       0.038 -    0.076: 43
       0.076 -    0.113: 32
       0.113 -    0.150: 18
       0.150 -    0.188: 9
  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 8.83e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.69e-01
  chirality model="   0" pdb=" CG  LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
            model="   0" pdb=" CD1 LEU A  93 "
            model="   0" pdb=" CD2 LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.77    0.18 2.00e-01 2.50e+01 8.41e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.123 2.00e-02 2.50e+03   4.87e-02 7.11e+01
        model="   0" pdb=" CG  TYR A  81 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.030 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.081 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.036 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.009 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.047 2.00e-02 2.50e+03   3.13e-02 2.93e+01
        model="   0" pdb=" CG  TYR A  91 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.070 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.059 2.00e-02 2.50e+03   2.51e-02 1.89e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.012 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 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.049 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.021 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 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.39 -     2.04: 34
        2.04 -     2.68: 3145
        2.68 -     3.32: 6422
        3.32 -     3.96: 7627
        3.96 -     4.60: 11508
  Nonbonded interactions: 28736
  Sorted by model distance:
  nonbonded model="   0" pdb="HG22 ILE A  77 "
            model="   0" pdb=" HE1 TYR A  81 "
     model   vdw
     1.394 2.270
  nonbonded model="   0" pdb=" HB  ILE A  71 "
            model="   0" pdb=" OH  TYR A  81 "
     model   vdw
     1.594 2.620
  nonbonded model="   0" pdb=" HB  ILE A  71 "
            model="   0" pdb=" HH  TYR A  81 "
     model   vdw
     1.633 2.270
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.670 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.672 1.850
  ... (remaining 28731 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: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 91
        1.23 -     1.43: 381
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.63e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.385 -0.031 1.10e-02 8.26e+03 8.10e+00
  bond model="   0" pdb=" CB  THR A  82 "
       model="   0" pdb=" OG1 THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.433  1.388  0.045 1.60e-02 3.91e+03 7.92e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.45e+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 6.87e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.54 -   106.17: 93
      106.17 -   111.79: 2503
      111.79 -   117.42: 468
      117.42 -   123.05: 792
      123.05 -   128.68: 223
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.51    4.09 1.00e+00 1.00e+00 1.67e+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  126.17    5.03 1.30e+00 5.92e-01 1.50e+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  126.24    4.96 1.30e+00 5.92e-01 1.45e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.09    3.51 1.00e+00 1.00e+00 1.23e+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  126.78    4.42 1.30e+00 5.92e-01 1.16e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 977
       17.97 -    35.95: 34
       35.95 -    53.92: 17
       53.92 -    71.90: 3
       71.90 -    89.87: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.39   18.61     0      5.00e+00 4.00e-02 1.39e+01
  dihedral model="   0" pdb=" N   ARG A 129 "
           model="   0" pdb=" CA  ARG A 129 "
           model="   0" pdb=" CB  ARG A 129 "
           model="   0" pdb=" CG  ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.15  -57.85     3      1.50e+01 4.44e-03 9.45e+00
  dihedral model="   0" pdb=" CA  LEU A  99 "
           model="   0" pdb=" CB  LEU A  99 "
           model="   0" pdb=" CG  LEU A  99 "
           model="   0" pdb=" CD1 LEU A  99 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  126.00   54.00     3      1.50e+01 4.44e-03 9.25e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 88
       0.050 -    0.101: 53
       0.101 -    0.151: 28
       0.151 -    0.201: 5
       0.201 -    0.251: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.38e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.068 2.00e-02 2.50e+03   2.92e-02 2.56e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.016 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   1.86e-02 1.04e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.046 2.00e-02 2.50e+03   1.79e-02 9.58e+00
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.012 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 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.028 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 "    0.015 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
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 86
        2.11 -     2.73: 3754
        2.73 -     3.35: 6157
        3.35 -     3.98: 7656
        3.98 -     4.60: 11286
  Nonbonded interactions: 28939
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ3 LYS A 113 "
            model="   0" pdb=" OE1 GLU A 120 "
     model   vdw
     1.487 1.850
  nonbonded model="   0" pdb="HD22 LEU A  93 "
            model="   0" pdb="HD12 LEU A  99 "
     model   vdw
     1.515 2.440
  nonbonded model="   0" pdb=" OG  SER A  76 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.540 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.544 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.547 1.850
  ... (remaining 28934 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 66
        1.23 -     1.42: 405
        1.42 -     1.62: 661
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 8.87e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.04e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.32e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.06e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 6.94e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.71 -   106.35: 126
      106.35 -   111.98: 2502
      111.98 -   117.62: 446
      117.62 -   123.26: 813
      123.26 -   128.90: 192
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.43    4.17 1.00e+00 1.00e+00 1.74e+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  126.40    4.80 1.30e+00 5.92e-01 1.36e+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  126.41    4.79 1.30e+00 5.92e-01 1.36e+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  116.22   -3.62 1.00e+00 1.00e+00 1.31e+01
  angle model="   0" pdb=" C   SER A  90 "
        model="   0" pdb=" N   TYR A  91 "
        model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta    sigma   weight residual
     121.70  128.00   -6.30 1.80e+00 3.09e-01 1.22e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.65: 958
       16.65 -    33.30: 47
       33.30 -    49.95: 20
       49.95 -    66.59: 5
       66.59 -    83.24: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  LEU A 119 "
           model="   0" pdb=" C   LEU A 119 "
           model="   0" pdb=" N   GLU A 120 "
           model="   0" pdb=" CA  GLU A 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.72   28.28     0      5.00e+00 4.00e-02 3.20e+01
  dihedral model="   0" pdb=" CA  GLY A  96 "
           model="   0" pdb=" C   GLY A  96 "
           model="   0" pdb=" N   SER A  97 "
           model="   0" pdb=" CA  SER A  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.65   20.35     0      5.00e+00 4.00e-02 1.66e+01
  dihedral model="   0" pdb=" CA  LYS A  85 "
           model="   0" pdb=" C   LYS A  85 "
           model="   0" pdb=" N   ILE A  86 "
           model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.76   19.24     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 76
       0.043 -    0.086: 50
       0.086 -    0.129: 35
       0.129 -    0.172: 12
       0.172 -    0.215: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  TYR A  89 "
            model="   0" pdb=" N   TYR A  89 "
            model="   0" pdb=" C   TYR A  89 "
            model="   0" pdb=" CB  TYR A  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality model="   0" pdb=" CA  ASP A  95 "
            model="   0" pdb=" N   ASP A  95 "
            model="   0" pdb=" C   ASP A  95 "
            model="   0" pdb=" CB  ASP A  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.76e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.09e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.167 2.00e-02 2.50e+03   7.10e-02 1.51e+02
        model="   0" pdb=" CG  TYR A  91 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.137 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.060 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.036 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.063 2.00e-02 2.50e+03   2.81e-02 2.38e+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 "   -0.010 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 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.062 2.00e-02 2.50e+03   2.46e-02 1.81e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 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 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.11 -     1.81: 12
        1.81 -     2.51: 1624
        2.51 -     3.20: 6821
        3.20 -     3.90: 7991
        3.90 -     4.60: 12236
  Nonbonded interactions: 28684
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ3 LYS A  79 "
            model="   0" pdb=" OH  TYR A  91 "
     model   vdw
     1.109 1.850
  nonbonded model="   0" pdb="HG21 THR A  82 "
            model="   0" pdb=" HB2 SER A  97 "
     model   vdw
     1.579 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.609 1.850
  nonbonded model="   0" pdb="HD13 LEU A 119 "
            model="   0" pdb=" HD2 LYS A 125 "
     model   vdw
     1.708 2.440
  nonbonded model="   0" pdb=" HB2 ASP A 116 "
            model="   0" pdb="HD12 LEU A 119 "
     model   vdw
     1.717 2.440
  ... (remaining 28679 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 0.72, per 1000 atoms: 0.32
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (37.471, 81.445, 48.362, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 87
        1.23 -     1.43: 385
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 5.99e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.91e+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 5.85e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.55e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.52e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.47 -   106.16: 96
      106.16 -   111.85: 2506
      111.85 -   117.54: 467
      117.54 -   123.23: 814
      123.23 -   128.92: 196
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.49    4.11 1.00e+00 1.00e+00 1.69e+01
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  128.50   -6.80 1.80e+00 3.09e-01 1.43e+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  116.25   -3.65 1.00e+00 1.00e+00 1.33e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.50    4.70 1.30e+00 5.92e-01 1.31e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.10   -3.50 1.00e+00 1.00e+00 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 972
       17.68 -    35.36: 39
       35.36 -    53.04: 17
       53.04 -    70.71: 4
       70.71 -    88.39: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  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  161.87   18.13     0      5.00e+00 4.00e-02 1.31e+01
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.40   17.60     0      5.00e+00 4.00e-02 1.24e+01
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.95  -16.05     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 73
       0.040 -    0.080: 41
       0.080 -    0.119: 35
       0.119 -    0.159: 22
       Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (81.482, 56.905, 49.757, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  0.159 -    0.199: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.88e-01
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.66e-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 8.42e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.071 2.00e-02 2.50e+03   2.90e-02 2.52e+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 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.052 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 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.054 2.00e-02 2.50e+03   2.33e-02 1.64e+01
        model="   0" pdb=" CG  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.002 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 "    0.018 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 "    0.012 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  ASP A  36 "    0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.067 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.31: 376
        2.31 -     2.88: 5143
        2.88 -     3.45: 5452
        3.45 -     4.03: 7145
        4.03 -     4.60: 10489
  Nonbonded interactions: 28605
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.737 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.763 1.850
  nonbonded model="   0" pdb=" HZ3 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.791 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.807 1.850
  ... (remaining 28600 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 65
        1.23 -     1.43: 407
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.63e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 6.82e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.30e+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 5.84e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.64e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.02 -   106.59: 136
      106.59 -   112.16: 2516
      112.16 -   117.73: 436
      117.73 -   123.30: 817
      123.30 -   128.87: 174
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.57    4.03 1.00e+00 1.00e+00 1.63e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.16    5.04 1.30e+00 5.92e-01 1.50e+01
  angle model="   0" pdb=" CB  HIS A 135 "
        model="   0" pdb=" CG  HIS A 135 "
        model="   0" pdb=" CD2 HIS A 135 "
      ideal   model   delta    sigma   weight residual
     131.20  126.49    4.71 1.30e+00 5.92e-01 1.31e+01
  angle model="   0" pdb=" 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  126.52    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  119.01    3.59 1.00e+00 1.00e+00 1.29e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.68: 975
       16.68 -    33.36: 44
       33.36 -    50.04: 10
       50.04 -    66.72: 3
       66.72 -    83.40: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.50   23.50     0      5.00e+00 4.00e-02 2.21e+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  159.85   20.15     0      5.00e+00 4.00e-02 1.62e+01
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.49   17.51     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 86
       0.051 -    0.102: 57
       0.102 -    0.153: 26
       0.153 -    0.204: 5
       0.204 -    0.254: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 136 "
            model="   0" pdb=" N   HIS A 136 "
            model="   0" pdb=" C   HIS A 136 "
            model="   0" pdb=" CB  HIS A 136 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.62e+00
  chirality model="   0" pdb=" CA  HIS A 134 "
            model="   0" pdb=" N   HIS A 134 "
            model="   0" pdb=" C   HIS A 134 "
            model="   0" pdb=" CB  HIS A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.06e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.078 2.00e-02 2.50e+03   3.11e-02 2.91e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.021 2.00e-02 2.50e+03   4.39e-02 1.92e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.076 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.055 2.00e-02 2.50e+03   2.44e-02 1.78e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.003 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 "    0.018 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 "    0.014 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.55 -     2.16: 115
        2.16 -     2.77: 4078
        2.77 -     3.38: 6062
        3.38 -     3.99: 7361
        3.99 -     4.60: 11027
  Nonbonded interactions: 28643
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.554 1.850
  nonbonded model="   0" pdb=" HB3 LEU A   3 "
            model="   0" pdb="HD11 LEU A  53 "
     model   vdw
     1.697 2.440
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.719 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.770 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.779 1.850
  ... (remaining 28638 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   16": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A ASP   88": "OD1" <-> "OD2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.00, per 1000 atoms: 0.45
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.378, 47.584, 54.546, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.01
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Symmetric amino acids flipped
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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:    0.020 (Z=  1.415)
  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:    3.810 (Z=  1.429)
  Mean delta:    0.544 (Z=  0.278)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   89.508
  Mean delta:   16.753

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.145
  Mean delta:    0.041

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.014
  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   0.020   2242  Z= 0.174
    Angle     :  1.024   4.673   4079  Z= 0.365
    Chirality :  0.041   0.145    176
    Planarity :  0.002   0.014    327
    Dihedral  : 13.783  89.508    769
    Min Nonbonded Distance : 1.656
  
  Molprobity Statistics.
    All-atom Clashscore : 7.21
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    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: -1.43 (0.66), residues: 137
    helix: -0.58 (0.57), residues: 70
    sheet:  None (None), residues: 0
    loop : -1.29 (0.73), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.006   0.002   PHE A  67 
   TYR   0.014   0.003   TYR A 111 
   ARG   0.006   0.001   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  67 
   TYR   0.012   0.003   TYR A 111 
   ARG   0.002   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A 137  HIS
   A 139  HIS

=================================== Summary ===================================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 102
        1.23 -     1.43: 370
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   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 7.65e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.22e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.76e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.73e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.61e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.23 -   106.80: 179
      106.80 -   112.37: 2510
      112.37 -   117.93: 411
      117.93 -   123.50: 824
      123.50 -   129.07: 155
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   THR A  82 "
        model="   0" pdb=" N   THR A  83 "
        model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  128.39   -6.69 1.80e+00 3.09e-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  118.94    3.66 1.00e+00 1.00e+00 1.34e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.55    4.65 1.30e+00 5.92e-01 1.28e+01
  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  116.14   -3.54 1.00e+00 1.00e+00 1.25e+01
  angle model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
        model="   0" pdb=" CA  LEU A 119 "
      ideal   model   delta    sigma   weight residual
     121.70  128.05   -6.35 1.80e+00 3.09e-01 1.24e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.68: 970
       17.68 -    35.36: 41
       35.36 -    53.04: 17
       53.04 -    70.72: 4
       70.72 -    88.41: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.39   25.61     0      5.00e+00 4.00e-02 2.62e+01
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.06   16.94     0      5.00e+00 4.00e-02 1.15e+01
  dihedral model="   0" pdb=" N   HIS A 136 "
           model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" CB  HIS A 136 "
           model="   0" pdb=" CG  HIS A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -104.07   44.07     3      1.50e+01 4.44e-03 7.93e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 80
       0.042 -    0.084: 43
       0.084 -    0.126: 35
       0.126 -    0.167: 15
       0.167 -    0.209: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LYS A  85 "
            model="   0" pdb=" N   LYS A  85 "
            model="   0" pdb=" C   LYS A  85 "
            model="   0" pdb=" CB  LYS A  85 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.09e+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 1.02e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.59e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.139 2.00e-02 2.50e+03   6.21e-02 1.16e+02
        model="   0" pdb=" CG  TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.125 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.056 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "   -0.034 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "    0.075 2.00e-02 2.50e+03   3.01e-02 2.73e+01
        model="   0" pdb=" CG  TYR A  89 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.010 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   2.55e-02 1.94e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.005 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 "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.19: 151
        2.19 -     2.79: 4324
        2.79 -     3.39: 6069
        3.39 -     4.00: 7346
        4.00 -     4.60: 11121
  Nonbonded interactions: 29011
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   TYR A  91 "
            model="   0" pdb=" H   LEU A  99 "
     model   vdw
     1.583 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.625 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=" OD2 ASP A  74 "
            model="   0" pdb=" HH  TYR A  91 "
     model   vdw
     1.724 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.740 1.850
  ... (remaining 29006 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.20, per 1000 atoms: 0.54
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.55, 78.75, 45.297, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  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: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.17e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 6.80e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.60e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.15e+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 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.77 -   107.42: 436
      107.42 -   113.07: 2329
      113.07 -   118.71: 421
      118.71 -   124.36: 811
      124.36 -   130.01: 82
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   GLY A  87 "
        model="   0" pdb=" N   ASP A  88 "
        model="   0" pdb=" CA  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     121.70  130.01   -8.31 1.80e+00 3.09e-01 2.13e+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  118.62    3.98 1.00e+00 1.00e+00 1.59e+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  126.14    5.06 1.30e+00 5.92e-01 1.51e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.37    4.83 1.30e+00 5.92e-01 1.38e+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  126.51    4.69 1.30e+00 5.92e-01 1.30e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 963
       17.40 -    34.80: 50
       34.80 -    52.21: 15
       52.21 -    69.61: 3
       69.61 -    87.01: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.24   35.76     0      5.00e+00 4.00e-02 5.12e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.95   30.05     0      5.00e+00 4.00e-02 3.61e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.43   29.57     0      5.00e+00 4.00e-02 3.50e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.037: 71
       0.037 -    0.073: 33
       0.073 -    0.109: 38
       0.109 -    0.145: 28
       0.145 -    0.181: 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 8.18e-01
  chirality model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" C   THR A  82 "
            model="   0" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.71   -0.18 2.00e-01 2.50e+01 8.10e-01
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.85e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.068 2.00e-02 2.50e+03   2.91e-02 2.54e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.058 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 "   -0.025 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 "   -0.014 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   2.20e-02 1.45e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 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 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  LEU A  93 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.10e+00
        model="   0" pdb=" C   LEU A  93 "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" O   LEU A  93 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" N   GLY A  94 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.07 -     1.77: 6
        1.77 -     2.48: 1464
        2.48 -     3.19: 6734
        3.19 -     3.89: 7950
        3.89 -     4.60: 12068
  Nonbonded interactions: 28222
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 LYS A  79 "
            model="   0" pdb=" HD1 TYR A  81 "
     model   vdw
     1.066 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.617 1.850
  nonbonded model="   0" pdb="HG22 ILE A  86 "
            model="   0" pdb=" H   GLY A  87 "
     model   vdw
     1.631 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.735 1.850
  ... (remaining 28217 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.21
  RMS(bonds)            =   0.0030
  RMS(angles)           =   1.02
  MolProbity score      =   1.70

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.34e+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 5.75e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.67e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.66e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.17e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.71 -   105.52: 56
      105.52 -   111.32: 2385
      111.32 -   117.12: 618
      117.12 -   122.93: 764
      122.93 -   128.73: 256
  Bond angle restraints: 4079
  Sorted by residual:
  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  125.99    5.21 1.30e+00 5.92e-01 1.61e+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  118.63    3.97 1.00e+00 1.00e+00 1.58e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.05    3.55 1.00e+00 1.00e+00 1.26e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.80    4.40 1.30e+00 5.92e-01 1.14e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.82    4.38 1.30e+00 5.92e-01 1.14e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.25: 966
       17.25 -    34.50: 47
       34.50 -    51.75: 11
       51.75 -    69.00: 6
       69.00 -    86.25: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A 130 "
           model="   0" pdb=" C   SER A 130 "
           model="   0" pdb=" N   ILE A 131 "
           model="   0" pdb=" CA  ILE A 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.14   27.86     0      5.00e+00 4.00e-02 3.10e+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  152.81   27.19     0      5.00e+00 4.00e-02 2.96e+01
  dihedral model="   0" pdb=" CA  HIS A 137 "
           model="   0" pdb=" C   HIS A 137 "
           model="   0" pdb=" N   HIS A 138 "
           model="   0" pdb=" CA  HIS A 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.25   23.75     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.057: 89
       0.057 -    0.113: 58
       0.113 -    0.169: 26
       0.169 -    0.225: 1
       0.225 -    0.281: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A 130 "
            model="   0" pdb=" N   SER A 130 "
            model="   0" pdb=" C   SER A 130 "
            model="   0" pdb=" CB  SER A 130 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.33e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.04e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.074 2.00e-02 2.50e+03   3.04e-02 2.77e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.008 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 "    0.057 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.047 2.00e-02 2.50e+03   1.84e-02 1.02e+01
        model="   0" pdb=" CG  TYR A  12 "    0.011 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 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 139 "    0.037 2.00e-02 2.50e+03   2.20e-02 9.66e+00
        model="   0" pdb=" CG  HIS A 139 "   -0.031 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 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 "    0.020 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 187
        2.23 -     2.82: 4606
        2.82 -     3.41: 5700
        3.41 -     4.01: 7178
        4.01 -     4.60: 10728
  Nonbonded interactions: 28399
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.636 1.850
  nonbonded model="   0" pdb=" HA  ILE A  71 "
            model="   0" pdb="HD12 ILE A  77 "
     model   vdw
     1.705 2.440
  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=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.737 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.776 1.850
  ... (remaining 28394 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  1.538)
  Mean delta:    0.004 (Z=  0.241)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.153 (Z=  1.979)
  Mean delta:    0.684 (Z=  0.330)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.007
  Max. delta:   67.606
  Mean delta:    8.237

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.143
  Mean delta:    0.037

                       ----------Planar groups----------                       

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.022
  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   2242  Z= 0.172
    Angle     :  1.059   6.153   4079  Z= 0.382
    Chirality :  0.037   0.143    176
    Planarity :  0.002   0.022    327
    Dihedral  :  8.980  67.606    769
    Min Nonbonded Distance : 1.493
  
  Molprobity Statistics.
    All-atom Clashscore : 13.07
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  1.46 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.37 (0.62), residues: 137
    helix: -0.53 (0.56), residues: 70
    sheet:  None (None), residues: 0
    loop : -1.26 (0.65), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 135 
   PHE   0.004   0.001   PHE A  15 
   TYR   0.007   0.002   TYR A  89 
   ARG   0.003   0.001   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 135 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.005   0.001   TYR A  12 
   ARG   0.002   0.000   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN
   A 136  HIS
   A 137  HIS

=================================== Summary ===================================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   1.46 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  13.07
  RMS(bonds)            =   0.0028
  RMS(angles)           =   1.06
  MolProbity score      =   1.79

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.12, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (42.156, 64.591, 61.705, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 0.73, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (56.304, 66.413, 42.372, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.14, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (37.509, 71.034, 44.683, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.18 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (49.079, 56.762, 55.31, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 93
        1.23 -     1.43: 379
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.87e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.60e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.19e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.15e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.10e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.06 -   105.82: 79
      105.82 -   111.58: 2429
      111.58 -   117.34: 545
      117.34 -   123.10: 813
      123.10 -   128.86: 213
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.70    3.90 1.00e+00 1.00e+00 1.52e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.34   -3.74 1.00e+00 1.00e+00 1.40e+01
  angle model="   0" pdb=" 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  126.46    4.74 1.30e+00 5.92e-01 1.33e+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  126.47    4.73 1.30e+00 5.92e-01 1.32e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.16    3.44 1.00e+00 1.00e+00 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 966
       17.14 -    34.27: 43
       34.27 -    51.41: 18
       51.41 -    68.55: 4
       68.55 -    85.68: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.52  -19.48     0      5.00e+00 4.00e-02 1.52e+01
  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  160.98   19.02     0      5.00e+00 4.00e-02 1.45e+01
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.80   17.20     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 68
       0.042 -    0.085: 51
       0.085 -    0.127: 37
       0.127 -    0.169: 16
       0.169 -    0.211: 4
  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    2.32    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    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  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.069 2.00e-02 2.50e+03   3.09e-02 2.86e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 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 "   -0.015 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 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.064 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.021 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        model="   0" pdb=" CG  ASP A  36 "    0.075 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.026 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.059 2.00e-02 2.50e+03   2.29e-02 1.57e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 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 "   -0.038 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        0.97 -     1.70: 7
        1.70 -     2.42: 1102
        2.42 -     3.15: 6845
        3.15 -     3.87: 8292
        3.87 -     4.60: 12958
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 29204
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   THR A  82 "
            model="   0" pdb=" HB2 LEU A  93 "
     model   vdw
     0.969 2.620
  nonbonded model="   0" pdb=" O   THR A  92 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.005 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.480 1.850
  nonbonded model="   0" pdb=" OG  SER A  76 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.500 1.850
  nonbonded model="   0" pdb="HG23 THR A  83 "
            model="   0" pdb=" HA  THR A  92 "
     model   vdw
     1.603 2.440
  ... (remaining 29199 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: 0.68
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.80 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 64
        1.23 -     1.42: 408
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.385 -0.031 1.10e-02 8.26e+03 7.88e+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 7.78e+00
  bond model="   0" pdb=" C   ILE A 131 "
       model="   0" pdb=" N   LEU A 132 "
    ideal  model  delta    sigma   weight residual
    1.329  1.364 -0.035 1.40e-02 5.10e+03 6.34e+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 6.18e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.27 -   106.04: 86
      106.04 -   111.80: 2508
      111.80 -   117.57: 484
      117.57 -   123.34: 815
      123.34 -   129.11: 186
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.32    4.28 1.00e+00 1.00e+00 1.83e+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  118.84    3.76 1.00e+00 1.00e+00 1.41e+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  126.42    4.78 1.30e+00 5.92e-01 1.35e+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  126.49    4.71 1.30e+00 5.92e-01 1.31e+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  116.00   -3.40 1.00e+00 1.00e+00 1.16e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.02: 964
       17.02 -    34.05: 47
       34.05 -    51.07: 16
       51.07 -    68.10: 4
       68.10 -    85.12: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ALA A 115 "
           model="   0" pdb=" C   ALA A 115 "
           model="   0" pdb=" N   ASP A 116 "
           model="   0" pdb=" CA  ASP A 116 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.46  -21.54     0      5.00e+00 4.00e-02 1.86e+01
  dihedral model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
           model="   0" pdb=" CB  HIS A 139 "
           model="   0" pdb=" CG  HIS A 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.29   58.29     3      1.50e+01 4.44e-03 9.46e+00
  dihedral model="   0" pdb=" N   ARG A 129 "
           model="   0" pdb=" CA  ARG A 129 "
           model="   0" pdb=" CB  ARG A 129 "
           model="   0" pdb=" CG  ARG A 129 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -122.61  -57.39     3      1.50e+01 4.44e-03 9.44e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 77
       0.043 -    0.086: 43
       0.086 -    0.128: 37
       0.128 -    0.171: 17
       0.171 -    0.214: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.14e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.70e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "   -0.076 2.00e-02 2.50e+03   3.10e-02 2.87e+01
        model="   0" pdb=" CG  TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "    0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "    0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.067 2.00e-02 2.50e+03   2.95e-02 2.61e+01
        model="   0" pdb=" CG  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.011 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 "   -0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.053 2.00e-02 2.50e+03   2.08e-02 1.30e+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 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.59 -     2.20: 167
        2.20 -     2.80: 4353
        2.80 -     3.40: 6096
        3.40 -     4.00: 7347
        4.00 -     4.60: 11179
  Nonbonded interactions: 29142
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.594 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.634 1.850
  nonbonded model="   0" pdb="HG22 ILE A  77 "
            model="   0" pdb=" HE2 TYR A  81 "
     model   vdw
     1.719 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.739 1.850
  ... (remaining 29137 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: 106
        1.23 -     1.43: 366
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.44e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.12e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.90e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.65e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.63e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.90 -   105.70: 66
      105.70 -   111.51: 2432
      111.51 -   117.31: 560
      117.31 -   123.11: 803
      123.11 -   128.91: 218
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.32    4.28 1.00e+00 1.00e+00 1.83e+01
  angle model="   0" pdb=" CB  HIS A 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.47    4.73 1.30e+00 5.92e-01 1.33e+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=" 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=" 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  126.91    4.29 1.30e+00 5.92e-01 1.09e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 958
       17.79 -    35.58: 55
       35.58 -    53.38: 15
       53.38 -    71.17: 3
       71.17 -    88.96: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  94 "
           model="   0" pdb=" C   GLY A  94 "
           model="   0" pdb=" N   ASP A  95 "
           model="   0" pdb=" CA  ASP A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.70  -26.30     0      5.00e+00 4.00e-02 2.77e+01
  dihedral model="   0" pdb=" CA  ASP A  74 "
           model="   0" pdb=" C   ASP A  74 "
           model="   0" pdb=" N   GLU A  75 "
           model="   0" pdb=" CA  GLU A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.07   22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.02   19.98     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 75
       0.047 -    0.094: 54
       0.094 -    0.140: 37
       0.140 -    0.187: 6
       0.187 -    0.234: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ASP A  74 "
            model="   0" pdb=" N   ASP A  74 "
            model="   0" pdb=" C   ASP A  74 "
            model="   0" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.165 2.00e-02 2.50e+03   7.44e-02 1.66e+02
        model="   0" pdb=" CG  TYR A  89 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.024 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.153 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.059 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.051 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.043 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.062 2.00e-02 2.50e+03   2.69e-02 2.17e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.016 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   1.89e-02 1.07e+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 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 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 "    0.031 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 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.03: 48
        2.03 -     2.67: 3147
        2.67 -     3.31: 6510
        3.31 -     3.96: 7833
        3.96 -     4.60: 11751
  Nonbonded interactions: 29289
  Sorted by model distance:
  nonbonded model="   0" pdb=" CE2 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.385 2.970
  nonbonded model="   0" pdb=" O   GLY A  80 "
            model="   0" pdb=" HB3 LEU A  93 "
     model   vdw
     1.444 2.620
  nonbonded model="   0" pdb=" HE2 TYR A  91 "
            model="   0" pdb="HD11 LEU A  99 "
     model   vdw
     1.569 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb="HG13 ILE A  77 "
     model   vdw
     1.625 2.620
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.651 1.850
  ... (remaining 29284 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Time building chain proxies: 1.05, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.973, 58.937, 40.241, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  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.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 117
        1.23 -     1.43: 355
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.07e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.20e+00
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.48e+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 6.33e+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 5.62e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.98 -   105.83: 70
      105.83 -   111.68: 2477
      111.68 -   117.53: 524
      117.53 -   123.38: 837
      123.38 -   129.23: 171
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.79    3.81 1.00e+00 1.00e+00 1.45e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.23   -3.63 1.00e+00 1.00e+00 1.32e+01
  angle model="   0" pdb=" 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  126.66    4.54 1.30e+00 5.92e-01 1.22e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.23   -4.83 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  116.04   -3.44 1.00e+00 1.00e+00 1.18e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.80: 964
       16.80 -    33.60: 45
       33.60 -    50.40: 14
       50.40 -    67.20: 8
       67.20 -    84.00: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.51   35.49     0      5.00e+00 4.00e-02 5.04e+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  155.69   24.31     0      5.00e+00 4.00e-02 2.36e+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  159.77   20.23     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.040: 72
       0.040 -    0.080: 46
       0.080 -    0.119: 34
       0.119 -    0.159: 19
       0.159 -    0.198: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.85e-01
  chirality model="   0" pdb=" CA  PRO A 117 "
            model="   0" pdb=" N   PRO A 117 "
            model="   0" pdb=" C   PRO A 117 "
            model="   0" pdb=" CB  PRO A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.42e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.18e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "    0.024 2.00e-02 2.50e+03   4.83e-02 2.34e+01
        model="   0" pdb=" CG  ASP A  36 "   -0.084 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "    0.031 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "    0.029 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.063 2.00e-02 2.50e+03   2.72e-02 2.22e+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 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.014 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.058 2.00e-02 2.50e+03   2.29e-02 1.57e+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 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.039 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.019 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.42 -     2.05: 56
        2.05 -     2.69: 3383
        2.69 -     3.33: 6539
        3.33 -     3.96: 7964
        3.96 -     4.60: 12058
  Nonbonded interactions: 30000
  Sorted by model distance:
  nonbonded model="   0" pdb=" HH  TYR A  89 "
            model="   0" pdb=" O   ASP A 103 "
     model   vdw
     1.418 1.850
  nonbonded model="   0" pdb=" HD3 LYS A  63 "
            model="   0" pdb=" HE2 TYR A  89 "
     model   vdw
     1.443 2.270
  nonbonded model="   0" pdb="HE22 GLN A  66 "
            model="   0" pdb="HG21 ILE A  86 "
     model   vdw
     1.505 2.270
  nonbonded model="   0" pdb=" HE2 PHE A  15 "
            model="   0" pdb="HD11 ILE A  86 "
     model   vdw
     1.514 2.270
  nonbonded model="   0" pdb=" HZ  PHE A  15 "
            model="   0" pdb=" OH  TYR A  91 "
     model   vdw
     1.538 2.450
  ... (remaining 29995 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== 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: 1.10
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.24 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 55
        1.23 -     1.42: 417
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 1.05e+01
  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 6.40e+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 6.10e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.94e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.72e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.32 -   106.07: 96
      106.07 -   111.81: 2482
      111.81 -   117.56: 502
      117.56 -   123.31: 801
      123.31 -   129.05: 198
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.40    4.20 1.00e+00 1.00e+00 1.77e+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  116.35   -3.75 1.00e+00 1.00e+00 1.41e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.14   -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  126.74    4.46 1.30e+00 5.92e-01 1.17e+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  119.24    3.36 1.00e+00 1.00e+00 1.13e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.04: 957
       17.04 -    34.08: 53
       34.08 -    51.11: 17
       51.11 -    68.15: 4
       68.15 -    85.19: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  138.30   41.70     0      5.00e+00 4.00e-02 6.95e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  142.86   37.14     0      5.00e+00 4.00e-02 5.52e+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  147.27   32.73     0      5.00e+00 4.00e-02 4.29e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.039: 70
       0.039 -    0.077: 38
       0.077 -    0.116: 37
       0.116 -    0.154: 27
     
  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  0.154 -    0.192: 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 9.22e-01
  chirality model="   0" pdb=" CA  TYR A  81 "
            model="   0" pdb=" N   TYR A  81 "
            model="   0" pdb=" C   TYR A  81 "
            model="   0" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.03e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.61e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.074 2.00e-02 2.50e+03   3.22e-02 3.11e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.016 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 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.066 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.024 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.025 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 "   -0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.022 2.00e-02 2.50e+03   4.39e-02 1.93e+01
        model="   0" pdb=" CG  ASP A  36 "    0.076 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.026 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   2.12e-02 1.34e+01
        model="   0" pdb=" CG  TYR A 111 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.035 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 "    0.018 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 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 223
        2.25 -     2.84: 4761
        2.84 -     3.42: 5727
        3.42 -     4.01: 7002
        4.01 -     4.60: 10530
  Nonbonded interactions: 28243
  Sorted by model distance:
  nonbonded model="   0" pdb="HG23 ILE A  77 "
            model="   0" pdb=" HD1 TYR A  81 "
     model   vdw
     1.659 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.725 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.727 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.731 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.747 1.850
  ... (remaining 28238 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.97
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.11 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (71.536, 44.316, 48.364, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 69
        1.23 -     1.43: 403
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 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 9.41e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.349 -0.028 1.00e-02 1.00e+04 8.03e+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 6.52e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.10e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.03e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.86 -   105.66: 68
      105.66 -   111.47: 2424
      111.47 -   117.27: 564
      117.27 -   123.07: 789
      123.07 -   128.87: 234
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  66 "
        model="   0" pdb=" CD  GLN A  66 "
        model="   0" pdb=" NE2 GLN A  66 "
      ideal   model   delta    sigma   weight residual
     122.60  118.89    3.71 1.00e+00 1.00e+00 1.38e+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  126.66    4.54 1.30e+00 5.92e-01 1.22e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.17    3.43 1.00e+00 1.00e+00 1.18e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.81    4.39 1.30e+00 5.92e-01 1.14e+01
  angle model="   0" pdb=" 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  115.88   -3.28 1.00e+00 1.00e+00 1.08e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.73: 948
       15.73 -    31.47: 62
       31.47 -    47.20: 16
       47.20 -    62.93: 4
       62.93 -    78.67: 3
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.26   26.74     0      5.00e+00 4.00e-02 2.86e+01
  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  156.93   23.07     0      5.00e+00 4.00e-02 2.13e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.69   22.31     0      5.00e+00 4.00e-02 1.99e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.040: 73
       0.040 -    0.079: 41
       0.079 -    0.117: 34
       0.117 -    0.156: 22
       0.156 -    0.194: 6
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.42e-01
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.92e-01
  chirality model="   0" pdb=" CB  THR A  82 "
            model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" OG1 THR A  82 "
            model="   0" pdb=" CG2 THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 6.96e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.073 2.00e-02 2.50e+03   3.18e-02 3.04e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.065 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 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.019 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.057 2.00e-02 2.50e+03   2.24e-02 1.51e+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 "    0.004 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 "   -0.037 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 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.019 2.00e-02 2.50e+03   3.88e-02 1.51e+01
        model="   0" pdb=" CG  ASP A  36 "    0.067 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.025 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.38 -     2.02: 38
        2.02 -     2.67: 3016
        2.67 -     3.31: 6445
        3.31 -     3.96: 7446
        3.96 -     4.60: 11250
  Nonbonded interactions: 28195
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB2 GLU A  49 "
            model="   0" pdb="HH11 ARG A 127 "
     model   vdw
     1.375 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.592 1.850
  nonbonded model="   0" pdb=" HE2 LYS A 113 "
            model="   0" pdb=" OE2 GLU A 120 "
     model   vdw
     1.662 2.620
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.684 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.699 1.850
  ... (remaining 28190 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.12 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 61
        1.23 -     1.42: 411
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 8.87e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.45e+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 6.43e+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 6.27e+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 6.22e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.79 -   105.62: 58
      105.62 -   111.45: 2424
      111.45 -   117.27: 577
      117.27 -   123.10: 798
      123.10 -   128.93: 222
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.36    4.24 1.00e+00 1.00e+00 1.80e+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  126.07    5.13 1.30e+00 5.92e-01 1.55e+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  126.51    4.69 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  119.10    3.50 1.00e+00 1.00e+00 1.22e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.93   -4.53 1.40e+00 5.10e-01 1.05e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 979
       17.80 -    35.60: 36
       35.60 -    53.40: 16
       53.40 -    71.19: 1
       71.19 -    88.99: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  HIS A 138 "
           model="   0" pdb=" C   HIS A 138 "
           model="   0" pdb=" N   HIS A 139 "
           model="   0" pdb=" CA  HIS A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.29   27.71     0      5.00e+00 4.00e-02 3.07e+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  152.74   27.26     0      5.00e+00 4.00e-02 2.97e+01
  dihedral model="   0" pdb=" CA  HIS A 136 "
           model="   0" pdb=" C   HIS A 136 "
           model="   0" pdb=" N   HIS A 137 "
           model="   0" pdb=" CA  HIS A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.81   25.19     0      5.00e+00 4.00e-02 2.54e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 70
       0.038 -    0.077: 43
       0.077 -    0.115: 40
       0.115 -    0.153: 21
       0.153 -    0.192: 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    2.32    0.19 2.00e-01 2.50e+01 9.19e-01
  chirality model="   0" pdb=" CG  LEU A  64 "
            model="   0" pdb=" CB  LEU A  64 "
            model="   0" pdb=" CD1 LEU A  64 "
            model="   0" pdb=" CD2 LEU A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.52e-01
  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   -2.74    0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.025 2.00e-02 2.50e+03   5.07e-02 2.57e+01
        model="   0" pdb=" CG  ASP A  36 "    0.088 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.032 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.031 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.059 2.00e-02 2.50e+03   2.53e-02 1.92e+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 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.051 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 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.013 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   2.44e-02 1.78e+01
        model="   0" pdb=" CG  TYR A 111 "    0.012 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 "    0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.044 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.008 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 104
        2.13 -     2.75: 3936
        2.75 -     3.37: 6053
        3.37 -     3.98: 7611
        3.98 -     4.60: 11256
  Nonbonded interactions: 28960
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.514 1.850
  nonbonded model="   0" pdb=" HG  SER A  76 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.578 2.100
  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  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.709 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.731 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: 0.98
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

  Time building chain proxies: 1.15, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (81.373, 54.529, 48.003, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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:    0.033 (Z=  2.369)
  Mean delta:    0.005 (Z=  0.287)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.268 (Z=  1.598)
  Mean delta:    0.581 (Z=  0.292)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   88.782
  Mean delta:   16.290

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.171
  Mean delta:    0.041

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.015
  Mean delta:    0.002

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 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   0.033   2242  Z= 0.205
    Angle     :  1.044   4.963   4079  Z= 0.373
    Chirality :  0.041   0.171    176
    Planarity :  0.002   0.015    327
    Dihedral  : 13.516  88.782    769
    Min Nonbonded Distance : 1.105
  
  Molprobity Statistics.
    All-atom Clashscore : 10.37
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  2.42 %
      Favored  : 96.77 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.23 (0.64), residues: 137
    helix: -0.35 (0.58), residues: 64
    sheet:  None (None), residues: 0
    loop : -1.21 (0.66), residues: 73
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.005   0.002   PHE A  45 
   TYR   0.011   0.003   TYR A  12 
   ARG   0.005   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 138 
   PHE   0.003   0.001   PHE A  45 
   TYR   0.008   0.002   TYR A  50 
   ARG   0.002   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN
   A 137  HIS

=================================== Summary ===================================

  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 8
        1.23 -     1.42: 461
        1.42 -     1.62: 663
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 134 "
       model="   0" pdb=" NE2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.321  1.343 -0.022 1.00e-02 1.00e+04 4.75e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.339 -0.018 1.00e-02 1.00e+04 3.40e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.339 -0.018 1.00e-02 1.00e+04 3.34e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.338 -0.017 1.00e-02 1.00e+04 2.88e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.28e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.82 -   106.60: 70
      106.60 -   112.38: 2658
      112.38 -   118.17: 434
      118.17 -   123.95: 844
      123.95 -   129.73: 73
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   GLY A  80 "
        model="   0" pdb=" N   TYR A  81 "
        model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     121.70  127.59   -5.89 1.80e+00 3.09e-01 1.07e+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  114.99   -2.39 1.00e+00 1.00e+00 5.72e+00
  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  120.77    1.83 1.00e+00 1.00e+00 3.36e+00
  angle model="   0" pdb=" N   TYR A  81 "
        model="   0" pdb=" CA  TYR A  81 "
        model="   0" pdb=" HA  TYR A  81 "
      ideal   model   delta    sigma   weight residual
     110.00  104.73    5.27 3.00e+00 1.11e-01 3.08e+00
  angle model="   0" pdb=" C   PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  103.80    5.20 3.00e+00 1.11e-01 3.00e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 989
       17.47 -    34.95: 28
       34.95 -    52.42: 7
       52.42 -    69.89: 3
       69.89 -    87.37: 6
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A   8 "
           model="   0" pdb=" CG  GLU A   8 "
           model="   0" pdb=" CD  GLU A   8 "
           model="   0" pdb=" OE1 GLU A   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.37  -87.37     1      3.00e+01 1.11e-03 1.02e+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   85.90  -85.90     1      3.00e+01 1.11e-03 9.90e+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   84.26  -84.26     1      3.00e+01 1.11e-03 9.60e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 89
       0.033 -    0.066: 49
       0.066 -    0.098: 32
       0.098 -    0.131: 3
       0.131 -    0.164: 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    2.60   -0.16 2.00e-01 2.50e+01 6.71e-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    2.58   -0.15 2.00e-01 2.50e+01 5.73e-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    2.58   -0.15 2.00e-01 2.50e+01 5.59e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "   -0.025 2.00e-02 2.50e+03   1.02e-02 3.11e+00
        model="   0" pdb=" CG  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.022 2.00e-02 2.50e+03   8.52e-03 2.18e+00
        model="   0" pdb=" CG  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "    0.008 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 "    0.003 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 "    0.021 2.00e-02 2.50e+03   7.99e-03 1.91e+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 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.000 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 "    0.007 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 "   -0.007 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
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 80
        2.15 -     2.76: 4123
        2.76 -     3.37: 5933
        3.37 -     3.99: 7276
        3.99 -     4.60: 11225
  Nonbonded interactions: 28637
  Sorted by model distance:
  nonbonded model="   0" pdb=" HE1 PHE A  15 "
            model="   0" pdb=" HH  TYR A  91 "
     model   vdw
     1.533 2.100
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" OH  TYR A  89 "
     model   vdw
     1.608 1.850
  nonbonded model="   0" pdb=" HB3 TYR A  91 "
            model="   0" pdb="HD12 LEU A  99 "
     model   vdw
     1.612 2.440
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" HH  TYR A  89 "
     model   vdw
     1.613 2.100
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.672 1.850
  ... (remaining 28632 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.10 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.14 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  10.37
  RMS(bonds)            =   0.0033
  RMS(angles)           =   1.04
  MolProbity score      =   1.54

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 2
        1.22 -     1.42: 455
        1.42 -     1.61: 675
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   HIS A 138 "
       model="   0" pdb=" N   HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.329  1.299  0.030 1.40e-02 5.10e+03 4.62e+00
  bond model="   0" pdb=" C   LYS A  85 "
       model="   0" pdb=" N   ILE A  86 "
    ideal  model  delta    sigma   weight residual
    1.329  1.300  0.029 1.40e-02 5.10e+03 4.31e+00
  bond model="   0" pdb=" C   LYS A  79 "
       model="   0" pdb=" N   GLY A  80 "
    ideal  model  delta    sigma   weight residual
    1.329  1.303  0.026 1.40e-02 5.10e+03 3.37e+00
  bond model="   0" pdb=" C   TYR A 111 "
       model="   0" pdb=" N   VAL A 112 "
    ideal  model  delta    sigma   weight residual
    1.329  1.306  0.023 1.40e-02 5.10e+03 2.77e+00
  bond model="   0" pdb=" C   HIS A 137 "
       model="   0" pdb=" N   HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.329  1.307  0.022 1.40e-02 5.10e+03 2.46e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.50 -   106.58: 48
      106.58 -   112.66: 2725
      112.66 -   118.74: 433
      118.74 -   124.82: 831
      124.82 -   130.90: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.97   -4.97 3.00e+00 1.11e-01 2.75e+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  113.86   -4.86 3.00e+00 1.11e-01 2.63e+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  113.83   -4.83 3.00e+00 1.11e-01 2.59e+00
  angle model="   0" pdb=" CB  PRO A 114 "
        model="   0" pdb=" CA  PRO A 114 "
        model="   0" pdb=" HA  PRO A 114 "
      ideal   model   delta    sigma   weight residual
     109.00  113.57   -4.57 3.00e+00 1.11e-01 2.32e+00
  angle model="   0" pdb=" CB  PRO A   6 "
        model="   0" pdb=" CA  PRO A   6 "
        model="   0" pdb=" HA  PRO A   6 "
      ideal   model   delta    sigma   weight residual
     109.00  113.46   -4.46 3.00e+00 1.11e-01 2.21e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 987
       17.84 -    35.68: 21
       35.68 -    53.52: 10
       53.52 -    71.37: 2
       71.37 -    89.21: 13
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  75 "
           model="   0" pdb=" CG  GLU A  75 "
           model="   0" pdb=" CD  GLU A  75 "
           model="   0" pdb=" OE1 GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.21  -89.21     1      3.00e+01 1.11e-03 1.05e+01
  dihedral model="   0" pdb=" CA  ASP A  47 "
           model="   0" pdb=" CB  ASP A  47 "
           model="   0" pdb=" CG  ASP A  47 "
           model="   0" pdb=" OD1 ASP A  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.82   54.82     1      2.00e+01 2.50e-03 1.02e+01
  dihedral model="   0" pdb=" CB  GLU A  16 "
           model="   0" pdb=" CG  GLU A  16 "
           model="   0" pdb=" CD  GLU A  16 "
           model="   0" pdb=" OE1 GLU A  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.17   87.17     1      3.00e+01 1.11e-03 1.01e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 130
       0.028 -    0.056: 26
       0.056 -    0.084: 9
       0.084 -    0.112: 8
       0.112 -    0.140: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  51 "
            model="   0" pdb=" N   ILE A  51 "
            model="   0" pdb=" C   ILE A  51 "
            model="   0" pdb=" CB  ILE A  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  chirality model="   0" pdb=" CA  ILE A  78 "
            model="   0" pdb=" N   ILE A  78 "
            model="   0" pdb=" C   ILE A  78 "
            model="   0" pdb=" CB  ILE A  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.67e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.20e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.011 2.00e-02 2.50e+03   4.16e-03 5.19e-01
        model="   0" pdb=" CG  TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "   -0.001 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.005 2.00e-02 2.50e+03   3.77e-03 4.27e-01
        model="   0" pdb=" CG  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.009 2.00e-02 2.50e+03   3.71e-03 4.12e-01
        model="   0" pdb=" CG  TYR A  12 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.005 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 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.19 -     1.87: 20
        1.87 -     2.55: 2075
        2.55 -     3.24: 6752
        3.24 -     3.92: 7887
        3.92 -     4.60: 12535
  Nonbonded interactions: 29269
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   LYS A  79 "
            model="   0" pdb=" HG1 THR A  83 "
     model   vdw
     1.191 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  88 "
            model="   0" pdb=" HD2 TYR A  89 "
     model   vdw
     1.390 2.450
  nonbonded model="   0" pdb=" HB3 LEU A   3 "
            model="   0" pdb="HD11 LEU A  53 "
     model   vdw
     1.391 2.440
  nonbonded model="   0" pdb=" O   VAL A 126 "
            model="   0" pdb=" HG  SER A 130 "
     model   vdw
     1.425 1.850
  nonbonded model="   0" pdb=" HB2 ASP A  47 "
            model="   0" pdb=" HD2 TYR A  50 "
     model   vdw
     1.644 2.270
  ... (remaining 29264 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: 111
        1.23 -     1.43: 361
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.352 -0.031 1.00e-02 1.00e+04 9.80e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.351 -0.030 1.00e-02 1.00e+04 9.14e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.348 -0.027 1.00e-02 1.00e+04 7.34e+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 6.69e+00
  bond model="   0" pdb=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.402 -0.028 1.10e-02 8.26e+03 6.36e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.95 -   105.76: 75
      105.76 -   111.57: 2433
      111.57 -   117.38: 552
      117.38 -   123.19: 818
      123.19 -   129.00: 201
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.73    3.87 1.00e+00 1.00e+00 1.49e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.60    4.60 1.30e+00 5.92e-01 1.25e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.15    3.45 1.00e+00 1.00e+00 1.19e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  129.00   -4.60 1.40e+00 5.10e-01 1.08e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.81   -3.21 1.00e+00 1.00e+00 1.03e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 966
       17.85 -    35.70: 44
       35.70 -    53.55: 16
       53.55 -    71.39: 6
       71.39 -    89.24: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.73   38.27     0      5.00e+00 4.00e-02 5.86e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.55   22.45     0      5.00e+00 4.00e-02 2.02e+01
  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  160.37   19.63     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.046: 75
       0.046 -    0.090: 52
       0.090 -    0.135: 33
       0.135 -    0.180: 11
       0.180 -    0.224: 5
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.058 2.00e-02 2.50e+03   2.46e-02 1.82e+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 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.021 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 "   -0.013 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   2.41e-02 1.75e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.043 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  LEU A  93 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        model="   0" pdb=" C   LEU A  93 "   -0.059 2.00e-02 2.50e+03
        model="   0" pdb=" O   LEU A  93 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" N   GLY A  94 "    0.020 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.17: 125
        2.17 -     2.78: 4213
        2.78 -     3.39: 6125
        3.39 -     3.99: 7333
        3.99 -     4.60: 11105
  Nonbonded interactions: 28901
  Sorted by model distance:
  nonbonded model="   0" pdb="HD23 LEU A 119 "
            model="   0" pdb="HD12 ILE A 122 "
     model   vdw
     1.568 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.680 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.738 1.850
  nonbonded model="   0" pdb=" HZ2 LYS A 109 "
            model="   0" pdb=" OD1 ASP A 110 "
     model   vdw
     1.750 1.850
  ... (remaining 28896 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (77.254, 42.268, 67.959, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.09 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 113
        1.23 -     1.43: 359
        1.43 -     1.63: 660
        1.63 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.350 -0.029 1.00e-02 1.00e+04 8.31e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.16e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.25e+00
  bond model="   0" pdb=" CE1 HIS A 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 6.22e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.77e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.25 -   106.79: 156
      106.79 -   112.33: 2529
      112.33 -   117.87: 404
      117.87 -   123.41: 825
      123.41 -   128.95: 165
  Bond angle restraints: 4079
  Sorted by residual:
  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  117.96   -5.36 1.00e+00 1.00e+00 2.87e+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  118.51    4.09 1.00e+00 1.00e+00 1.67e+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  118.94    3.66 1.00e+00 1.00e+00 1.34e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.64    4.56 1.30e+00 5.92e-01 1.23e+01
  angle model="   0" pdb=" 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  126.94    4.26 1.30e+00 5.92e-01 1.07e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.81: 967
       16.81 -    33.61: 44
       33.61 -    50.42: 18
       50.42 -    67.23: 2
       67.23 -    84.04: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ASP A  74 "
           model="   0" pdb=" C   ASP A  74 "
           model="   0" pdb=" N   GLU A  75 "
           model="   0" pdb=" CA  GLU A  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.20   19.80     0      5.00e+00 4.00e-02 1.57e+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 -162.43  -17.57     0      5.00e+00 4.00e-02 1.24e+01
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -165.70  -14.30     0      5.00e+00 4.00e-02 8.18e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.045: 76
       0.045 -    0.089: 45
       0.089 -    0.134: 39
       0.134 -    0.178: 13
       0.178 -    0.222: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality model="   0" pdb=" CA  ASP A  74 "
            model="   0" pdb=" N   ASP A  74 "
            model="   0" pdb=" C   ASP A  74 "
            model="   0" pdb=" CB  ASP A  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality model="   0" pdb=" CA  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
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.081 2.00e-02 2.50e+03   3.18e-02 3.04e+01
        model="   0" pdb=" CG  TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.002 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   2.62e-02 2.06e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.047 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.023 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 "   -0.007 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.056 2.00e-02 2.50e+03   2.31e-02 1.60e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.044 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 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.12: 96
        2.12 -     2.74: 3858
        2.74 -     3.36: 6385
        3.36 -     3.98: 7851
        3.98 -     4.60: 11691
  Nonbonded interactions: 29881
  Sorted by model distance:
  nonbonded model="   0" pdb="HG12 ILE A  77 "
            model="   0" pdb="HD22 LEU A  93 "
     model   vdw
     1.495 2.440
  nonbonded model="   0" pdb=" O   GLY A  80 "
            model="   0" pdb=" O   LEU A  93 "
     model   vdw
     1.567 2.800
  nonbonded model="   0" pdb=" HD1 TYR A  91 "
            model="   0" pdb="HD23 LEU A  99 "
     model   vdw
     1.583 2.270
  nonbonded model="   0" pdb=" HA  TYR A  81 "
            model="   0" pdb=" O   LEU A  93 "
     model   vdw
     1.601 2.620
  nonbonded model="   0" pdb="HE22 GLN A  66 "
            model="   0" pdb="HD12 ILE A  86 "
     model   vdw
     1.707 2.270
  ... (remaining 29876 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Time building chain proxies: 0.99, per 1000 atoms: 0.45
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (38.772, 73.06, 73.858, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  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: 82
        1.23 -     1.43: 390
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 6.50e+00
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.93e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.85e+00
  bond model="   0" pdb=" CZ  ARG A  21 "
       model="   0" pdb=" NH2 ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.330  1.299  0.031 1.30e-02 5.92e+03 5.84e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.77e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.07 -   105.96: 81
      105.96 -   111.85: 2521
      111.85 -   117.74: 477
      117.74 -   123.63: 873
      123.63 -   129.53: 127
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   LYS A  85 "
        model="   0" pdb=" N   ILE A  86 "
        model="   0" pdb=" CA  ILE A  86 "
      ideal   model   delta    sigma   weight residual
     121.70  129.53   -7.83 1.80e+00 3.09e-01 1.89e+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  126.44    4.76 1.30e+00 5.92e-01 1.34e+01
  angle model="   0" pdb=" C   THR A  83 "
        model="   0" pdb=" N   GLU A  84 "
        model="   0" pdb=" CA  GLU A  84 "
      ideal   model   delta    sigma   weight residual
     121.70  128.23   -6.53 1.80e+00 3.09e-01 1.32e+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  116.19   -3.59 1.00e+00 1.00e+00 1.29e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.15   -3.55 1.00e+00 1.00e+00 1.26e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.15: 967
       17.15 -    34.31: 47
       34.31 -    51.46: 13
       51.46 -    68.61: 5
       68.61 -    85.77: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.59   22.41     0      5.00e+00 4.00e-02 2.01e+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  164.14   15.86     0      5.00e+00 4.00e-02 1.01e+01
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.20   15.80     0      5.00e+00 4.00e-02 9.98e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 71
       0.043 -    0.085: 52
       0.085 -    0.127: 33
       0.127 -    0.169: 16
       0.169 -    0.211: 4
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.11e+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=" 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 7.48e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  89 "   -0.128 2.00e-02 2.50e+03   5.60e-02 9.39e+01
        model="   0" pdb=" CG  TYR A  89 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  89 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  89 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  89 "    0.019 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  89 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  89 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  89 "   -0.110 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  89 "    0.048 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  89 "    0.053 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  89 "    0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  89 "    0.027 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.127 2.00e-02 2.50e+03   5.38e-02 8.68e+01
        model="   0" pdb=" CG  TYR A  81 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.031 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.103 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.054 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.029 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.040 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.084 2.00e-02 2.50e+03   3.64e-02 3.98e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.018 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 "    0.011 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 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.073 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.033 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.024 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.20: 164
        2.20 -     2.80: 4398
        2.80 -     3.40: 6060
        3.40 -     4.00: 7300
        4.00 -     4.60: 10920
  Nonbonded interactions: 28842
  Sorted by model distance:
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.601 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.630 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.686 1.850
  nonbonded model="   0" pdb="HG21 ILE A  77 "
            model="   0" pdb=" HD2 TYR A  91 "
     model   vdw
     1.692 2.270
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.706 2.440
  ... (remaining 28837 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.923)
  Mean delta:    0.012 (Z=  0.644)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003 (Z=  0.002)
  Max. delta:    7.689 (Z=  3.957)
  Mean delta:    1.681 (Z=  0.902)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   147.63    32.37  5.00e+00  4.19e+01   6.5*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   151.01    28.99  5.00e+00  3.36e+01   5.8*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   152.28    27.72  5.00e+00  3.07e+01   5.5*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   154.03    25.97  5.00e+00  2.70e+01   5.2*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   157.27    22.73  5.00e+00  2.07e+01   4.5*sigma
   A  87  GLY  CA
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        180.00  -159.44   -20.56  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.007
  Max. delta:   77.154
  Mean delta:   13.334

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.196
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.084
  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      :  0.009   0.040   2242  Z= 0.459
    Angle     :  1.593   7.689   4079  Z= 0.686
    Chirality :  0.081   0.196    176
    Planarity :  0.009   0.063    327
    Dihedral  : 11.699  77.154    769
    Min Nonbonded Distance : 1.334
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  5.84 %
      Allowed  :  5.84 %
      Favored  : 88.32 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  3.23 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.76 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.50 (0.69), residues: 137
    helix:  0.65 (0.53), residues: 80
    sheet:  None (None), residues: 0
    loop : -1.80 (0.84), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.003   PHE A  67 
   TYR   0.075   0.010   TYR A 111 
   ARG   0.068   0.014   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.063   0.012   TYR A 111 
   ARG   0.007   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   5.84 %
                favored =  88.32 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.59
  MolProbity score      =   2.13

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  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.

  Time building chain proxies: 0.73, per 1000 atoms: 0.33
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.388, 58.226, 60.306, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   ILE A  78 "
       model="   0" pdb=" N   LYS A  79 "
    ideal  model  delta    sigma   weight residual
    1.329  1.370 -0.041 1.40e-02 5.10e+03 8.70e+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 6.83e+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 6.41e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.13e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.381 -0.027 1.10e-02 8.26e+03 6.00e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.39 -   106.04: 90
      106.04 -   111.70: 2476
      111.70 -   117.36: 490
      117.36 -   123.01: 793
      123.01 -   128.67: 230
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CA  GLY A  80 "
        model="   0" pdb=" C   GLY A  80 "
        model="   0" pdb=" N   TYR A  81 "
      ideal   model   delta    sigma   weight residual
     116.20  124.58   -8.38 2.00e+00 2.50e-01 1.75e+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  118.51    4.09 1.00e+00 1.00e+00 1.67e+01
  angle model="   0" pdb=" N   GLY A  80 "
        model="   0" pdb=" CA  GLY A  80 "
        model="   0" pdb=" C   GLY A  80 "
      ideal   model   delta    sigma   weight residual
     113.30  124.21  -10.91 2.90e+00 1.19e-01 1.41e+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  126.54    4.66 1.30e+00 5.92e-01 1.28e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.07    3.53 1.00e+00 1.00e+00 1.25e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 968
       17.91 -    35.82: 48
       35.82 -    53.73: 10
       53.73 -    71.63: 6
       71.63 -    89.54: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  GLY A  80 "
           model="   0" pdb=" C   GLY A  80 "
           model="   0" pdb=" N   TYR A  81 "
           model="   0" pdb=" CA  TYR A  81 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.88  -28.12     0      5.00e+00 4.00e-02 3.16e+01
  dihedral model="   0" pdb=" CA  SER A  76 "
           model="   0" pdb=" C   SER A  76 "
           model="   0" pdb=" N   ILE A  77 "
           model="   0" pdb=" CA  ILE A  77 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.94   22.06     0      5.00e+00 4.00e-02 1.95e+01
  dihedral model="   0" pdb=" CA  LYS A  79 "
           model="   0" pdb=" C   LYS A  79 "
           model="   0" pdb=" N   GLY A  80 "
           model="   0" pdb=" CA  GLY A  80 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.92  -21.08     0      5.00e+00 4.00e-02 1.78e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 86
       0.055 -    0.109: 57
       0.109 -    0.164: 27
       0.164 -    0.218: 3
       0.218 -    0.273: 3
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.86e+00
  chirality model="   0" pdb=" CA  TYR A  81 "
            model="   0" pdb=" N   TYR A  81 "
            model="   0" pdb=" C   TYR A  81 "
            model="   0" pdb=" CB  TYR A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" C   THR A  82 "
            model="   0" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "   -0.065 2.00e-02 2.50e+03   2.86e-02 2.45e+01
        model="   0" pdb=" CG  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.058 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.023 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 "    0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  PHE A  15 "    0.066 2.00e-02 2.50e+03   2.64e-02 2.08e+01
        model="   0" pdb=" CG  PHE A  15 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 PHE A  15 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 PHE A  15 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 PHE A  15 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 PHE A  15 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  PHE A  15 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 PHE A  15 "   -0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 PHE A  15 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 PHE A  15 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 PHE A  15 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HZ  PHE A  15 "    0.032 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   2.33e-02 1.62e+01
        model="   0" pdb=" CG  TYR A 111 "    0.012 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 "    0.005 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 "   -0.042 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 184
        2.22 -     2.81: 4404
        2.81 -     3.41: 5876
        3.41 -     4.00: 7115
        4.00 -     4.60: 10657
  Nonbonded interactions: 28236
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.620 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.689 1.850
  nonbonded model="   0" pdb=" O   GLY A  80 "
            model="   0" pdb=" HA3 GLY A  94 "
     model   vdw
     1.707 2.620
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.756 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.806 1.850
  ... (remaining 28231 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

============================== Collecting inputs ==============================


  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.03
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.17 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.95
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.07 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 71
        1.23 -     1.43: 401
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.09e+00
  bond model="   0" pdb=" ND1 HIS A 135 "
       model="   0" pdb=" CE1 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.81e+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 5.63e+00
  bond model="   0" pdb=" ND1 HIS A  43 "
       model="   0" pdb=" CE1 HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.51e+00
  bond model="   0" pdb=" ND1 HIS A 136 "
       model="   0" pdb=" CE1 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.28e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.48 -   106.17: 101
      106.17 -   111.85: 2503
      111.85 -   117.53: 465
      117.53 -   123.21: 809
      123.21 -   128.89: 201
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.60    4.00 1.00e+00 1.00e+00 1.60e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.17    3.43 1.00e+00 1.00e+00 1.18e+01
  angle model="   0" pdb=" 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  115.96   -3.36 1.00e+00 1.00e+00 1.13e+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  115.88   -3.28 1.00e+00 1.00e+00 1.08e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.97    4.23 1.30e+00 5.92e-01 1.06e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 974
       17.84 -    35.68: 36
       35.68 -    53.52: 19
       53.52 -    71.36: 3
       71.36 -    89.20: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.91   23.09     0      5.00e+00 4.00e-02 2.13e+01
  dihedral model="   0" pdb=" CA  THR A  82 "
           model="   0" pdb=" C   THR A  82 "
           model="   0" pdb=" N   THR A  83 "
           model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.72   21.28     0      5.00e+00 4.00e-02 1.81e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.50   15.50     0      5.00e+00 4.00e-02 9.61e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 80
       0.048 -    0.096: 54
       0.096 -    0.143: 32
       0.143 -    0.191: 7
       0.191 -    0.239: 3
  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    2.29    0.24 2.00e-01 2.50e+01 1.42e+00
  chirality model="   0" pdb=" CA  HIS A 138 "
            model="   0" pdb=" N   HIS A 138 "
            model="   0" pdb=" C   HIS A 138 "
            model="   0" pdb=" CB  HIS A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.070 2.00e-02 2.50e+03   3.06e-02 2.80e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.014 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 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.062 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 "   -0.022 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 "   -0.020 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "   -0.061 2.00e-02 2.50e+03   2.38e-02 1.70e+01
        model="   0" pdb=" CG  TYR A  12 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "   -0.007 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 "    0.019 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 "    0.008 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  ASP A  36 "   -0.020 2.00e-02 2.50e+03   4.09e-02 1.67e+01
        model="   0" pdb=" CG  ASP A  36 "    0.071 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.48 -     2.11: 80
        2.11 -     2.73: 3717
        2.73 -     3.35: 6259
        3.35 -     3.98: 7602
        3.98 -     4.60: 11469
  Nonbonded interactions: 29127
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.481 1.850
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.682 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.699 1.850
  nonbonded model="   0" pdb="HD11 LEU A  64 "
            model="   0" pdb=" HE3 LYS A 101 "
     model   vdw
     1.705 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.755 1.850
  ... (remaining 29122 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: 66
        1.23 -     1.43: 406
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 8.78e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.298  0.032 1.30e-02 5.92e+03 5.88e+00
  bond model="   0" pdb=" C   MET A 128 "
       model="   0" pdb=" N   ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.034 1.40e-02 5.10e+03 5.87e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.46e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.344 -0.023 1.00e-02 1.00e+04 5.14e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.05 -   105.83: 76
      105.83 -   111.61: 2443
      111.61 -   117.38: 552
      117.38 -   123.16: 797
      123.16 -   128.93: 211
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.43    4.17 1.00e+00 1.00e+00 1.74e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.03    3.57 1.00e+00 1.00e+00 1.28e+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  126.89    4.31 1.30e+00 5.92e-01 1.10e+01
  angle model="   0" pdb=" CD  ARG A  21 "
        model="   0" pdb=" NE  ARG A  21 "
        model="   0" pdb=" CZ  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     124.40  128.90   -4.50 1.40e+00 5.10e-01 1.03e+01
  angle model="   0" pdb=" CA  ASP A 118 "
        model="   0" pdb=" C   ASP A 118 "
        model="   0" pdb=" N   LEU A 119 "
      ideal   model   delta    sigma   weight residual
     116.20  122.49   -6.29 2.00e+00 2.50e-01 9.88e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 973
       18.00 -    36.00: 42
       36.00 -    54.00: 12
       54.00 -    72.00: 4
       72.00 -    89.99: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  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  160.37   19.63     0      5.00e+00 4.00e-02 1.54e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.13   18.87     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 63
       0.036 -    0.073: 47
       0.073 -    0.109: 37
       0.109 -    0.145: 23
       0.145 -    0.182: 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 8.24e-01
  chirality model="   0" pdb=" CA  SER A  76 "
            model="   0" pdb=" N   SER A  76 "
            model="   0" pdb=" C   SER A  76 "
            model="   0" pdb=" CB  SER A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.87e-01
  chirality model="   0" pdb=" CA  ALA A 115 "
            model="   0" pdb=" N   ALA A 115 "
            model="   0" pdb=" C   ALA A 115 "
            model="   0" pdb=" CB  ALA A 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.65   -0.17 2.00e-01 2.50e+01 6.86e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.074 2.00e-02 2.50e+03   3.12e-02 2.92e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.061 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.024 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 "   -0.017 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "   -0.059 2.00e-02 2.50e+03   2.32e-02 1.62e+01
        model="   0" pdb=" CG  TYR A 111 "    0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.004 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 "    0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "    0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.059 2.00e-02 2.50e+03   2.26e-02 1.53e+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 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.035 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.020 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 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 149
        2.18 -     2.79: 4358
        2.79 -     3.39: 6197
        3.39 -     4.00: 7600
        4.00 -     4.60: 11452
  Nonbonded interactions: 29756
  Sorted by model distance:
  nonbonded model="   0" pdb=" O   ASP A 118 "
            model="   0" pdb=" H   ILE A 122 "
     model   vdw
     1.578 1.850
  nonbonded model="   0" pdb=" HG  SER A  76 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.627 2.100
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.676 1.850
  nonbonded model="   0" pdb=" HG  SER A  17 "
            model="   0" pdb=" OE2 GLU A  84 "
     model   vdw
     1.711 1.850
  nonbonded model="   0" pdb=" O   ILE A 122 "
            model="   0" pdb=" H   VAL A 126 "
     model   vdw
     1.742 1.850
  ... (remaining 29751 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.042 (Z=  2.617)
  Mean delta:    0.012 (Z=  0.632)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.58     4.02  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.131 (Z=  4.025)
  Mean delta:    1.566 (Z=  0.861)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:   75.636
  Mean delta:   12.447

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.217
  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:    0.010

============================= 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   0.042   2242  Z= 0.450
    Angle     :  1.524   7.131   4079  Z= 0.659
    Chirality :  0.077   0.217    176
    Planarity :  0.008   0.038    327
    Dihedral  : 10.807  75.636    769
    Min Nonbonded Distance : 1.635
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    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:  0.64 (0.67), residues: 137
    helix:  0.30 (0.51), residues: 82
    sheet:  None (None), residues: 0
    loop :  0.94 (0.88), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.070   0.010   TYR A  50 
   ARG   0.040   0.009   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.009   0.003   PHE A  67 
   TYR   0.058   0.012   TYR A  50 
   ARG   0.004   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.956)
  Mean delta:    0.012 (Z=  0.643)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    9.476 (Z=  4.191)
  Mean delta:    1.671 (Z=  0.885)

                      ----------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   141.99    38.01  5.00e+00  5.78e+01   7.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   144.39    35.61  5.00e+00  5.07e+01   7.1*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   145.11    34.89  5.00e+00  4.87e+01   7.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   145.47    34.53  5.00e+00  4.77e+01   6.9*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -150.67   -29.33  5.00e+00  3.44e+01   5.9*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   151.88    28.12  5.00e+00  3.16e+01   5.6*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   152.95    27.05  5.00e+00  2.93e+01   5.4*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   154.51    25.49  5.00e+00  2.60e+01   5.1*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   156.10    23.90  5.00e+00  2.28e+01   4.8*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   156.30    23.70  5.00e+00  2.25e+01   4.7*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   156.80    23.20  5.00e+00  2.15e+01   4.6*sigma

  Min. delta:    0.006
  Max. delta:   83.312
  Mean delta:   12.913

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.244
  Mean delta:    0.079

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.043
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.039   2242  Z= 0.458
    Angle     :  1.596   9.476   4079  Z= 0.680
    Chirality :  0.079   0.244    176
    Planarity :  0.007   0.043    327
    Dihedral  : 11.807  83.312    769
    Min Nonbonded Distance : 1.753
  
  Molprobity Statistics.
    All-atom Clashscore : 3.61
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  : 10.22 %
      Favored  : 85.40 %
    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 : 3.05 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.07 (0.71), residues: 137
    helix: -0.66 (0.53), residues: 76
    sheet:  None (None), residues: 0
    loop : -0.58 (0.92), residues: 61
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.064   0.008   TYR A  50 
   ARG   0.037   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.054   0.010   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.798)
  Mean delta:    0.012 (Z=  0.636)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   130.12    -8.42  1.80e+00  2.19e+01   4.7*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.41     4.19  1.00e+00  1.76e+01   4.2*sigma
   A 137  HIS  CB
   A 137  HIS  CG
   A 137  HIS  CD2       131.20   125.79     5.41  1.30e+00  1.73e+01   4.2*sigma
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        121.70   128.99    -7.29  1.80e+00  1.64e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    8.422 (Z=  4.679)
  Mean delta:    1.741 (Z=  0.942)

                      ----------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   149.82    30.18  5.00e+00  3.64e+01   6.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   151.66    28.34  5.00e+00  3.21e+01   5.7*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -152.97   -27.03  5.00e+00  2.92e+01   5.4*sigma
   A  84  GLU  CA
   A  84  GLU  C
   A  85  LYS  N
   A  85  LYS  CA        180.00   153.40    26.60  5.00e+00  2.83e+01   5.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   154.34    25.66  5.00e+00  2.63e+01   5.1*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   155.99    24.01  5.00e+00  2.31e+01   4.8*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   156.74    23.26  5.00e+00  2.16e+01   4.7*sigma
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   158.80    21.20  5.00e+00  1.80e+01   4.2*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00  -159.52   -20.48  5.00e+00  1.68e+01   4.1*sigma
   A  98  SER  CA
   A  98  SER  C
   A  99  LEU  N
   A  99  LEU  CA        180.00   159.61    20.39  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.008
  Max. delta:   88.158
  Mean delta:   13.473

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.249
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.453
    Angle     :  1.632   8.604   4079  Z= 0.710
    Chirality :  0.082   0.249    176
    Planarity :  0.008   0.047    327
    Dihedral  : 12.216  89.915    769
    Min Nonbonded Distance : 1.642
  
  Molprobity Statistics.
    All-atom Clashscore : 10.82
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  8.76 %
      Favored  : 87.59 %
    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: -0.34 (0.69), residues: 137
    helix: -0.16 (0.56), residues: 70
    sheet:  None (None), residues: 0
    loop : -0.13 (0.81), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.034   0.006   PHE A  67 
   TYR   0.055   0.009   TYR A 111 
   ARG   0.037   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.020   0.006   PHE A  67 
   TYR   0.046   0.011   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.494)
  Mean delta:    0.011 (Z=  0.599)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.659 (Z=  3.519)
  Mean delta:    1.593 (Z=  0.864)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.026
  Max. delta:   83.684
  Mean delta:   12.896

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.188
  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:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.426
    Angle     :  1.541   6.659   4079  Z= 0.663
    Chirality :  0.075   0.188    176
    Planarity :  0.008   0.042    327
    Dihedral  : 11.965  83.684    769
    Min Nonbonded Distance : 1.633
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.20 (0.69), residues: 137
    helix:  0.34 (0.51), residues: 81
    sheet:  None (None), residues: 0
    loop :  0.04 (0.91), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.015   0.003   PHE A  45 
   TYR   0.077   0.013   TYR A  89 
   ARG   0.036   0.011   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.009   0.003   PHE A  45 
   TYR   0.062   0.015   TYR A  89 
   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      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.52
  MolProbity score      =   1.44

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   3.65 %
                favored =  87.59 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =  10.82
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.63
  MolProbity score      =   2.45

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   4.38 %
                favored =  85.40 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   3.61
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.60
  MolProbity score      =   1.80

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.54
  MolProbity score      =   2.04

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.01, per 1000 atoms: 0.46
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.075, 57.255, 82.277, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

============================== Collecting inputs ==============================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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.

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: 50
        1.23 -     1.42: 422
        1.42 -     1.62: 660
        1.62 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CZ  ARG A 127 "
       model="   0" pdb=" NH2 ARG A 127 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.72e+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 6.54e+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 6.06e+00
  bond model="   0" pdb=" ND1 HIS A 138 "
       model="   0" pdb=" CE1 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.99e+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 5.58e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
       99.75 -   105.59: 52
      105.59 -   111.43: 2422
      111.43 -   117.27: 578
      117.27 -   123.10: 812
      123.10 -   128.94: 215
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.56    4.04 1.00e+00 1.00e+00 1.63e+01
  angle model="   0" pdb=" CB  HIS A  43 "
        model="   0" pdb=" CG  HIS A  43 "
        model="   0" pdb=" CD2 HIS A  43 "
      ideal   model   delta    sigma   weight residual
     131.20  126.59    4.61 1.30e+00 5.92e-01 1.26e+01
  angle model="   0" pdb=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.07    3.53 1.00e+00 1.00e+00 1.24e+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  126.88    4.32 1.30e+00 5.92e-01 1.11e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  115.86   -3.26 1.00e+00 1.00e+00 1.06e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 975
       17.38 -    34.77: 38
       34.77 -    52.15: 16
       52.15 -    69.53: 3
       69.53 -    86.91: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.81   16.19     0      5.00e+00 4.00e-02 1.05e+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 -129.60  -50.40     3      1.50e+01 4.44e-03 8.90e+00
  dihedral model="   0" pdb=" N   MET A 128 "
           model="   0" pdb=" CA  MET A 128 "
           model="   0" pdb=" CB  MET A 128 "
           model="   0" pdb=" CG  MET A 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -104.83   44.83     3      1.50e+01 4.44e-03 8.06e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 76
       0.039 -    0.078: 40
       0.078 -    0.117: 35
       0.117 -    0.156: 23
       0.156 -    0.195: 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    2.32    0.19 2.00e-01 2.50e+01 9.47e-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 8.01e-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 5.45e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.052 2.00e-02 2.50e+03   2.02e-02 1.22e+01
        model="   0" pdb=" CG  TYR A  12 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  12 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  12 "    0.032 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  12 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  12 "   -0.006 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.048 2.00e-02 2.50e+03   2.00e-02 1.20e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.003 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 "   -0.018 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 "   -0.007 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 "    0.044 2.00e-02 2.50e+03   1.75e-02 9.18e+00
        model="   0" pdb=" CG  TYR A 111 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.028 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.018 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.23: 195
        2.23 -     2.82: 4538
        2.82 -     3.41: 5784
        3.41 -     4.01: 7304
        4.01 -     4.60: 10715
  Nonbonded interactions: 28536
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  47 "
            model="   0" pdb=" HZ1 LYS A 113 "
     model   vdw
     1.636 1.850
  nonbonded model="   0" pdb=" HB3 GLU A  49 "
            model="   0" pdb="HH11 ARG A 127 "
     model   vdw
     1.642 2.270
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.729 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.757 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.782 1.850
  ... (remaining 28531 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.039 (Z=  2.914)
  Mean delta:    0.012 (Z=  0.627)

                        ----------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  1.65e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.910 (Z=  4.067)
  Mean delta:    1.587 (Z=  0.874)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   159.29    20.71  5.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.044
  Max. delta:   87.562
  Mean delta:   12.286

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.202
  Mean delta:    0.073

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.046
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.446
    Angle     :  1.531   6.910   4079  Z= 0.666
    Chirality :  0.073   0.202    176
    Planarity :  0.008   0.046    327
    Dihedral  : 11.034  87.562    769
    Min Nonbonded Distance : 1.581
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  0.73 %
      Favored  : 98.54 %
    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 : 0.00 %
  
  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:  0.43 (0.68), residues: 137
    helix:  0.09 (0.51), residues: 83
    sheet: -2.08 (1.16), residues: 12
    loop :  2.02 (1.00), residues: 42
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.015   0.003   PHE A  45 
   TYR   0.081   0.009   TYR A  50 
   ARG   0.038   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.011   0.003   PHE A  67 
   TYR   0.067   0.011   TYR A  50 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.026 (Z=  1.838)
  Mean delta:    0.004 (Z=  0.274)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.767 (Z=  1.369)
  Mean delta:    0.723 (Z=  0.344)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.003
  Max. delta:   86.353
  Mean delta:   12.275

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.135
  Mean delta:    0.040

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.023
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.026   2242  Z= 0.195
    Angle     :  1.083   5.206   4079  Z= 0.391
    Chirality :  0.040   0.135    176
    Planarity :  0.002   0.023    327
    Dihedral  : 11.583  86.353    769
    Min Nonbonded Distance : 1.599
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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:  0.59 (0.71), residues: 137
    helix:  0.26 (0.59), residues: 71
    sheet:  None (None), residues: 0
    loop :  0.80 (0.81), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.005   0.002   PHE A  15 
   TYR   0.019   0.003   TYR A  91 
   ARG   0.015   0.003   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 138 
   PHE   0.002   0.001   PHE A  67 
   TYR   0.015   0.003   TYR A  91 
   ARG   0.002   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  98.54 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   7.66
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.53
  MolProbity score      =   1.71

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0032
  RMS(angles)           =   1.08
  MolProbity score      =   1.71

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

============================== Collecting inputs ==============================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.048 (Z=  2.979)
  Mean delta:    0.012 (Z=  0.624)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.212 (Z=  4.167)
  Mean delta:    1.651 (Z=  0.903)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 119  LEU  CA
   A 119  LEU  C
   A 120  GLU  N
   A 120  GLU  CA        180.00   151.72    28.28  5.00e+00  3.20e+01   5.7*sigma
   A  96  GLY  CA
   A  96  GLY  C
   A  97  SER  N
   A  97  SER  CA        180.00   159.65    20.35  5.00e+00  1.66e+01   4.1*sigma

  Min. delta:    0.047
  Max. delta:   83.242
  Mean delta:   13.368

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.215
  Mean delta:    0.078

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.075
  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      :  0.009   0.048   2242  Z= 0.444
    Angle     :  1.567   7.212   4079  Z= 0.683
    Chirality :  0.078   0.215    176
    Planarity :  0.009   0.071    327
    Dihedral  : 12.015  83.242    769
    Min Nonbonded Distance : 1.109
  
  Molprobity Statistics.
    All-atom Clashscore : 10.37
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  8.03 %
      Favored  : 89.05 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.86 (0.65), residues: 137
    helix: -0.12 (0.50), residues: 80
    sheet:  None (None), residues: 0
    loop : -1.11 (0.84), residues: 57
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 134 
   PHE   0.016   0.005   PHE A  67 
   TYR   0.167   0.016   TYR A  91 
   ARG   0.043   0.012   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 134 
   PHE   0.008   0.004   PHE A  67 
   TYR   0.136   0.020   TYR A  91 
   ARG   0.005   0.002   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A 100  GLN

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.98 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


============================== Collecting inputs ==============================


============================== Collecting inputs ==============================

  Ramachandran outliers =   2.92 %
                favored =  89.05 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =  10.37
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.57
  MolProbity score      =   2.50

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 75
        1.23 -     1.43: 397
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" 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 7.48e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.384 -0.030 1.10e-02 8.26e+03 7.24e+00
  bond model="   0" pdb=" C   ALA A 124 "
       model="   0" pdb=" N   LYS A 125 "
    ideal  model  delta    sigma   weight residual
    1.329  1.366 -0.037 1.40e-02 5.10e+03 6.91e+00
  bond model="   0" pdb=" CG  HIS A 138 "
       model="   0" pdb=" CD2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 6.79e+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 6.31e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.37 -   106.08: 98
      106.08 -   111.79: 2484
      111.79 -   117.50: 481
      117.50 -   123.22: 815
      123.22 -   128.93: 201
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.52    4.08 1.00e+00 1.00e+00 1.67e+01
  angle model="   0" pdb=" 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  126.46    4.74 1.30e+00 5.92e-01 1.33e+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  126.49    4.71 1.30e+00 5.92e-01 1.31e+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=" OE1 GLN A 100 "
        model="   0" pdb=" CD  GLN A 100 "
        model="   0" pdb=" NE2 GLN A 100 "
      ideal   model   delta    sigma   weight residual
     122.60  119.10    3.50 1.00e+00 1.00e+00 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 958
       17.09 -    34.17: 54
       34.17 -    51.26: 17
       51.26 -    68.34: 3
       68.34 -    85.43: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  125.96   54.04     0      5.00e+00 4.00e-02 1.17e+02
  dihedral model="   0" pdb=" CA  TYR A  91 "
           model="   0" pdb=" C   TYR A  91 "
           model="   0" pdb=" N   THR A  92 "
           model="   0" pdb=" CA  THR A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.41   39.59     0      5.00e+00 4.00e-02 6.27e+01
  dihedral model="   0" pdb=" CA  TYR A  89 "
           model="   0" pdb=" C   TYR A  89 "
           model="   0" pdb=" N   SER A  90 "
           model="   0" pdb=" CA  SER A  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.94   36.06     0      5.00e+00 4.00e-02 5.20e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 68
       0.037 -    0.074: 40
       0.074 -    0.111: 34
       0.111 -    0.148: 24
       0.148 -    0.185: 10
  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 8.55e-01
  chirality model="   0" pdb=" CA  ILE A  86 "
            model="   0" pdb=" N   ILE A  86 "
            model="   0" pdb=" C   ILE A  86 "
            model="   0" pdb=" CB  ILE A  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.32e-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    2.68   -0.17 2.00e-01 2.50e+01 7.20e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.057 2.00e-02 2.50e+03   2.27e-02 1.55e+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 "    0.005 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 "   -0.015 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 "   -0.005 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   1.99e-02 1.18e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 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 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.041 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.013 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  91 "    0.051 2.00e-02 2.50e+03   1.94e-02 1.13e+01
        model="   0" pdb=" CG  TYR A  91 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  91 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  91 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  91 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  91 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  91 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  91 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  91 "    0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.27 -     1.93: 16
        1.93 -     2.60: 2255
        2.60 -     3.27: 6695
        3.27 -     3.93: 7807
        3.93 -     4.60: 11481
  Nonbonded interactions: 28254
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB2 LYS A  85 "
            model="   0" pdb=" HE1 TYR A  89 "
     model   vdw
     1.265 2.270
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.744 1.850
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.762 1.850
  nonbonded model="   0" pdb=" O   LEU A  61 "
            model="   0" pdb=" HG  SER A  65 "
     model   vdw
     1.848 1.850
  nonbonded model="   0" pdb=" O   ASP A  88 "
            model="   0" pdb=" H   SER A  90 "
     model   vdw
     1.853 1.850
  ... (remaining 28249 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A PHE   45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

============================== Collecting inputs ==============================

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.042 (Z=  2.633)
  Mean delta:    0.012 (Z=  0.631)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  36  ASP  CA
   A  36  ASP  CB
   A  36  ASP  CG        112.60   116.75    -4.15  1.00e+00  1.72e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.550 (Z=  4.148)
  Mean delta:    1.620 (Z=  0.889)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -156.39   -23.61  5.00e+00  2.23e+01   4.7*sigma

  Min. delta:    0.002
  Max. delta:   67.373
  Mean delta:   12.442

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.210
  Mean delta:    0.080

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.091
  Mean delta:    0.014

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  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   2242  Z= 0.449
    Angle     :  1.554   6.550   4079  Z= 0.676
    Chirality :  0.080   0.210    176
    Planarity :  0.010   0.083    327
    Dihedral  : 11.182  67.373    769
    Min Nonbonded Distance : 1.438
  
  Molprobity Statistics.
    All-atom Clashscore : 14.43
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.84 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  2.42 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.16 (0.71), residues: 137
    helix:  0.57 (0.53), residues: 84
    sheet:  None (None), residues: 0
    loop : -1.13 (0.93), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 136 
   PHE   0.100   0.014   PHE A  15 
   TYR   0.209   0.021   TYR A  81 
   ARG   0.040   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 136 
   PHE   0.065   0.014   PHE A  15 
   TYR   0.172   0.025   TYR A  81 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.038 (Z=  2.577)
  Mean delta:    0.012 (Z=  0.634)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.906 (Z=  3.573)
  Mean delta:    1.603 (Z=  0.879)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   148.71    31.29  5.00e+00  3.92e+01   6.3*sigma

  Min. delta:    0.021
  Max. delta:   82.557
  Mean delta:   13.346

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.188
  Mean delta:    0.076

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.052
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.038   2242  Z= 0.451
    Angle     :  1.550   6.906   4079  Z= 0.672
    Chirality :  0.076   0.188    176
    Planarity :  0.008   0.049    327
    Dihedral  : 11.787  82.557    769
    Min Nonbonded Distance : 1.394
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.92 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  3.23 %
      Favored  : 91.94 %
    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: -0.09 (0.72), residues: 137
    helix:  0.41 (0.53), residues: 80
    sheet: -5.51 (0.57), residues: 10
    loop :  0.78 (1.03), residues: 47
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.011   0.003   PHE A  45 
   TYR   0.123   0.017   TYR A  81 
   ARG   0.037   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 138 
   PHE   0.009   0.003   PHE A  67 
   TYR   0.100   0.020   TYR A  81 
   ARG   0.004   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  94.16 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =  14.43
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.55
  MolProbity score      =   2.35

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.00 %
                favored =  97.08 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.55
  MolProbity score      =   2.06

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  2.882)
  Mean delta:    0.012 (Z=  0.638)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.96    -5.36  1.00e+00  2.87e+01   5.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.424 (Z=  5.359)
  Mean delta:    1.576 (Z=  0.861)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.020
  Max. delta:   81.930
  Mean delta:   11.929

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.222
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.043
  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   2242  Z= 0.454
    Angle     :  1.532   6.529   4079  Z= 0.661
    Chirality :  0.081   0.222    176
    Planarity :  0.008   0.036    327
    Dihedral  : 11.295  84.036    769
    Min Nonbonded Distance : 1.495
  
  Molprobity Statistics.
    All-atom Clashscore : 17.13
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    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: -0.09 (0.68), residues: 137
    helix:  0.29 (0.51), residues: 84
    sheet:  None (None), residues: 0
    loop : -0.46 (0.89), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.016   0.005   PHE A  15 
   TYR   0.081   0.012   TYR A  81 
   ARG   0.036   0.008   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   0.066   0.014   TYR A  81 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== 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: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.043 (Z=  3.070)
  Mean delta:    0.012 (Z=  0.655)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        121.70   130.81    -9.11  1.80e+00  2.56e+01   5.1*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.008 (Z=  0.004)
  Max. delta:    9.114 (Z=  5.063)
  Mean delta:    1.674 (Z=  0.919)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00  -134.38   -45.62  5.00e+00  8.33e+01   9.1*sigma
   A 118  ASP  CA
   A 118  ASP  C
   A 119  LEU  N
   A 119  LEU  CA        180.00   156.34    23.66  5.00e+00  2.24e+01   4.7*sigma

  Min. delta:    0.003
  Max. delta:   88.517
  Mean delta:   13.099

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.241
  Mean delta:    0.076

                       ----------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      :  0.009   0.043   2242  Z= 0.466
    Angle     :  1.584   9.114   4079  Z= 0.693
    Chirality :  0.076   0.241    176
    Planarity :  0.008   0.035    327
    Dihedral  : 11.637  88.517    769
    Min Nonbonded Distance : 1.654
  
  Molprobity Statistics.
    All-atom Clashscore : 4.06
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  5.65 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 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:  0.27 (0.71), residues: 137
    helix:  0.47 (0.55), residues: 78
    sheet:  None (None), residues: 0
    loop : -0.03 (0.88), residues: 59
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 137 
   PHE   0.022   0.005   PHE A  45 
   TYR   0.070   0.010   TYR A  50 
   ARG   0.037   0.007   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 137 
   PHE   0.013   0.005   PHE A  45 
   TYR   0.058   0.011   TYR A  50 
   ARG   0.002   0.000   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.937)
  Mean delta:    0.012 (Z=  0.630)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.980 (Z=  4.031)
  Mean delta:    1.603 (Z=  0.876)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   156.50    23.50  5.00e+00  2.21e+01   4.7*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   159.85    20.15  5.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.007
  Max. delta:   83.395
  Mean delta:   11.279

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.254
  Mean delta:    0.076

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.044
  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   0.040   2242  Z= 0.448
    Angle     :  1.541   6.980   4079  Z= 0.668
    Chirality :  0.076   0.254    176
    Planarity :  0.007   0.044    327
    Dihedral  : 10.093  83.395    769
    Min Nonbonded Distance : 1.554
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  0.81 %
      Favored  : 97.58 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 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:  0.70 (0.72), residues: 137
    helix:  0.21 (0.53), residues: 81
    sheet: -2.60 (1.16), residues: 10
    loop :  2.22 (1.06), residues: 46
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 134 
   PHE   0.026   0.006   PHE A  45 
   TYR   0.078   0.010   TYR A 111 
   ARG   0.033   0.008   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 134 
   PHE   0.017   0.005   PHE A  45 
   TYR   0.064   0.012   TYR A 111 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.002)
  Max. delta:    0.045 (Z=  2.938)
  Mean delta:    0.012 (Z=  0.635)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    7.105 (Z=  4.089)
  Mean delta:    1.564 (Z=  0.861)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.010
  Max. delta:   89.869
  Mean delta:   12.767

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.251
  Mean delta:    0.076

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.042
  Mean delta:    0.010

============================= 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   0.045   2242  Z= 0.452
    Angle     :  1.522   7.105   4079  Z= 0.659
    Chirality :  0.076   0.251    176
    Planarity :  0.007   0.032    327
    Dihedral  : 11.734  89.869    769
    Min Nonbonded Distance : 1.487
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  0.73 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  3.23 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.32 (0.67), residues: 137
    helix:  0.45 (0.53), residues: 83
    sheet:  None (None), residues: 0
    loop :  0.05 (0.82), residues: 54
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.017   0.005   PHE A  15 
   TYR   0.068   0.009   TYR A  50 
   ARG   0.036   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.011   0.005   PHE A  67 
   TYR   0.056   0.011   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 =  97.81 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  17.13
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.53
  MolProbity score      =   1.78

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.13, per 1000 atoms: 0.51
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (41.083, 53.316, 60.885, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =   4.06
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.58
  MolProbity score      =   1.54

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.678)
  Mean delta:    0.012 (Z=  0.623)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   130.01    -8.31  1.80e+00  2.13e+01   4.6*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.619 (Z=  4.617)
  Mean delta:    1.727 (Z=  0.908)

                      ----------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   144.24    35.76  5.00e+00  5.12e+01   7.2*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   149.95    30.05  5.00e+00  3.61e+01   6.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   150.43    29.57  5.00e+00  3.50e+01   5.9*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   152.33    27.67  5.00e+00  3.06e+01   5.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   153.90    26.10  5.00e+00  2.73e+01   5.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   156.51    23.49  5.00e+00  2.21e+01   4.7*sigma

  Min. delta:    0.012
  Max. delta:   87.012
  Mean delta:   13.260

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.181
  Mean delta:    0.077

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.044
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.443
    Angle     :  1.613   8.619   4079  Z= 0.690
    Chirality :  0.077   0.181    176
    Planarity :  0.009   0.043    327
    Dihedral  : 11.876  87.012    769
    Min Nonbonded Distance : 1.066
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  :  7.30 %
      Favored  : 86.13 %
    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 : 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: -0.61 (0.70), residues: 137
    helix:  0.44 (0.52), residues: 82
    sheet:  None (None), residues: 0
    loop : -1.69 (0.90), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.020   0.004   PHE A  45 
   TYR   0.068   0.010   TYR A  50 
   ARG   0.036   0.011   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.014   0.005   PHE A  67 
   TYR   0.056   0.012   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  98.54 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.52
  MolProbity score      =   1.48

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.446)
  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   118.49     4.11  1.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    6.800 (Z=  4.106)
  Mean delta:    1.619 (Z=  0.884)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.019
  Max. delta:   88.391
  Mean delta:   13.096

                       ----------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:    0.046
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.448
    Angle     :  1.552   6.800   4079  Z= 0.673
    Chirality :  0.078   0.199    176
    Planarity :  0.008   0.046    327
    Dihedral  : 11.505  88.391    769
    Min Nonbonded Distance : 1.732
  
  Molprobity Statistics.
    All-atom Clashscore : 4.51
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  2.19 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.03 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.58 (0.69), residues: 137
    helix: -0.15 (0.49), residues: 88
    sheet:  None (None), residues: 0
    loop : -0.58 (1.00), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.003   PHE A  45 
   TYR   0.071   0.010   TYR A 111 
   ARG   0.038   0.010   ARG A  58 

  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   0.011   TYR A 111 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.54
  MolProbity score      =   1.46

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.766)
  Mean delta:    0.012 (Z=  0.614)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.175 (Z=  3.715)
  Mean delta:    1.626 (Z=  0.879)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   154.39    25.61  5.00e+00  2.62e+01   5.1*sigma

  Min. delta:    0.004
  Max. delta:   88.405
  Mean delta:   12.285

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.209
  Mean delta:    0.076

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  91  TYR  CB
   A  91  TYR  CG
   A  91  TYR  CD1
   A  91  TYR  CD2
   A  91  TYR  CE1
   A  91  TYR  CE2
   A  91  TYR  CZ
   A  91  TYR  OH            0.065       0.112       83.37   5.6*sigma

  Min. delta:    0.000
  Max. delta:    0.071
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.041   2242  Z= 0.437
    Angle     :  1.564   7.175   4079  Z= 0.673
    Chirality :  0.076   0.209    176
    Planarity :  0.009   0.062    327
    Dihedral  : 11.435  88.405    769
    Min Nonbonded Distance : 1.583
  
  Molprobity Statistics.
    All-atom Clashscore : 11.72
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  4.38 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  2.42 %
      Favored  : 97.58 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.33 (0.68), residues: 137
    helix:  0.55 (0.52), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.10 (0.88), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.139   0.018   TYR A  91 
   ARG   0.058   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.012   0.004   PHE A  67 
   TYR   0.112   0.021   TYR A  91 
   ARG   0.007   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.518)
  Mean delta:    0.012 (Z=  0.605)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 135  HIS  CB
   A 135  HIS  CG
   A 135  HIS  CD2       131.20   125.99     5.21  1.30e+00  1.61e+01   4.0*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.475 (Z=  4.009)
  Mean delta:    1.627 (Z=  0.879)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 130  SER  CA
   A 130  SER  C
   A 131  ILE  N
   A 131  ILE  CA        180.00   152.14    27.86  5.00e+00  3.10e+01   5.6*sigma
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   152.81    27.19  5.00e+00  2.96e+01   5.4*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   156.25    23.75  5.00e+00  2.26e+01   4.8*sigma
   A 133  GLU  CA
   A 133  GLU  C
   A 134  HIS  N
   A 134  HIS  CA        180.00   157.26    22.74  5.00e+00  2.07e+01   4.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   159.00    21.00  5.00e+00  1.76e+01   4.2*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   159.39    20.61  5.00e+00  1.70e+01   4.1*sigma

  Min. delta:    0.010
  Max. delta:   86.254
  Mean delta:   14.295

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.281
  Mean delta:    0.078

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.047
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.431
    Angle     :  1.557   6.475   4079  Z= 0.671
    Chirality :  0.078   0.281    176
    Planarity :  0.007   0.047    327
    Dihedral  : 12.058  86.254    769
    Min Nonbonded Distance : 1.636
  
  Molprobity Statistics.
    All-atom Clashscore : 5.86
    Ramachandran Plot:
      Outliers :  3.65 %
      Allowed  :  5.11 %
      Favored  : 91.24 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.74 (0.72), residues: 137
    helix: -0.25 (0.56), residues: 69
    sheet: -3.64 (1.01), residues: 12
    loop :  0.25 (0.97), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.027   0.007   PHE A  45 
   TYR   0.074   0.009   TYR A 111 
   ARG   0.033   0.007   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.017   0.007   PHE A  45 
   TYR   0.063   0.010   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 =   6.57 %
                favored =  86.13 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.61
  MolProbity score      =   2.09

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.92 %
                favored =  94.89 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.51
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.55
  MolProbity score      =   1.74

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   0.73 %
                favored =  94.89 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  11.72
  RMS(bonds)            =   0.0083
  RMS(angles)           =   1.56
  MolProbity score      =   1.94

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   3.65 %
                favored =  91.24 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   5.86
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.56
  MolProbity score      =   2.22

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

Symmetry information was not found, putting molecule in P1 box.

                   ----------Processing PDB file(s)----------                  

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.808)
  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   118.32     4.28  1.00e+00  1.83e+01   4.3*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.654 (Z=  4.280)
  Mean delta:    1.604 (Z=  0.884)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00  -158.46   -21.54  5.00e+00  1.86e+01   4.3*sigma

  Min. delta:    0.002
  Max. delta:   85.121
  Mean delta:   12.783

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.214
  Mean delta:    0.077

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.045
  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   0.038   2242  Z= 0.456
    Angle     :  1.541   6.654   4079  Z= 0.671
    Chirality :  0.077   0.214    176
    Planarity :  0.008   0.041    327
    Dihedral  : 11.445  85.121    769
    Min Nonbonded Distance : 1.594
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  2.19 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  4.03 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.16 (0.68), residues: 137
    helix:  0.44 (0.52), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.80 (0.87), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.020   0.005   PHE A  67 
   TYR   0.076   0.011   TYR A  81 
   ARG   0.039   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.061   0.013   TYR A  81 
   ARG   0.005   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  3.240)
  Mean delta:    0.012 (Z=  0.628)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.40     4.20  1.00e+00  1.77e+01   4.2*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    7.174 (Z=  4.203)
  Mean delta:    1.692 (Z=  0.905)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   138.30    41.70  5.00e+00  6.95e+01   8.3*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   142.86    37.14  5.00e+00  5.52e+01   7.4*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   147.27    32.73  5.00e+00  4.29e+01   6.5*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   155.42    24.58  5.00e+00  2.42e+01   4.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   156.74    23.26  5.00e+00  2.16e+01   4.7*sigma
   A  83  THR  CA
   A  83  THR  C
   A  84  GLU  N
   A  84  GLU  CA        180.00   159.45    20.55  5.00e+00  1.69e+01   4.1*sigma

  Min. delta:    0.003
  Max. delta:   85.190
  Mean delta:   13.278

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.192
  Mean delta:    0.079

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.048
  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   2242  Z= 0.447
    Angle     :  1.596   7.174   4079  Z= 0.687
    Chirality :  0.079   0.192    176
    Planarity :  0.009   0.048    327
    Dihedral  : 11.736  85.190    769
    Min Nonbonded Distance : 1.659
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  5.84 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  1.61 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.46 (0.71), residues: 137
    helix:  0.27 (0.51), residues: 86
    sheet:  None (None), residues: 0
    loop : -1.19 (0.98), residues: 51
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.022   0.005   PHE A  67 
   TYR   0.074   0.009   TYR A  50 
   ARG   0.038   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.012   0.005   PHE A  67 
   TYR   0.062   0.010   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 =   0.73 %
                favored =  97.08 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.54
  MolProbity score      =   1.78

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
  Ramachandran outliers =   4.38 %
                favored =  89.78 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.60
  MolProbity score      =   2.39

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (55.987, 46.135, 57.593, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR   89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR   91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.622)
  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:    7.079 (Z=  3.905)
  Mean delta:    1.641 (Z=  0.895)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   85.681
  Mean delta:   13.181

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.211
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.068
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.471
    Angle     :  1.570   7.079   4079  Z= 0.681
    Chirality :  0.081   0.211    176
    Planarity :  0.009   0.051    327
    Dihedral  : 11.587  85.681    769
    Min Nonbonded Distance : 0.969
  
  Molprobity Statistics.
    All-atom Clashscore : 8.12
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  5.11 %
      Favored  : 94.89 %
    Rotamer:
      Outliers :  4.84 %
      Allowed  :  3.23 %
      Favored  : 91.94 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.33 (0.69), residues: 137
    helix:  0.15 (0.51), residues: 90
    sheet:  None (None), residues: 0
    loop : -0.71 (0.95), residues: 47
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.014   0.004   PHE A  45 
   TYR   0.069   0.010   TYR A  50 
   ARG   0.056   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.058   0.012   TYR A  50 
   ARG   0.006   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.038 (Z=  2.728)
  Mean delta:    0.012 (Z=  0.649)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.32     4.28  1.00e+00  1.83e+01   4.3*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    7.000 (Z=  4.282)
  Mean delta:    1.630 (Z=  0.885)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  94  GLY  CA
   A  94  GLY  C
   A  95  ASP  N
   A  95  ASP  CA        180.00  -153.70   -26.30  5.00e+00  2.77e+01   5.3*sigma
   A  74  ASP  CA
   A  74  ASP  C
   A  75  GLU  N
   A  75  GLU  CA        180.00   157.07    22.93  5.00e+00  2.10e+01   4.6*sigma

  Min. delta:    0.005
  Max. delta:   88.960
  Mean delta:   13.553

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.234
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.078
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  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   0.038   2242  Z= 0.462
    Angle     :  1.565   7.186   4079  Z= 0.675
    Chirality :  0.081   0.234    176
    Planarity :  0.009   0.074    327
    Dihedral  : 12.056  88.960    769
    Min Nonbonded Distance : 1.385
  
  Molprobity Statistics.
    All-atom Clashscore : 18.49
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  7.30 %
      Favored  : 92.70 %
    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: -0.05 (0.72), residues: 137
    helix:  0.39 (0.53), residues: 82
    sheet:  None (None), residues: 0
    loop : -0.54 (0.98), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.018   0.003   PHE A  45 
   TYR   0.165   0.016   TYR A  89 
   ARG   0.057   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.011   0.004   PHE A  45 
   TYR   0.133   0.019   TYR A  89 
   ARG   0.006   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  94.89 %
  Rotamer outliers      =   4.84 %
  C-beta deviations     =     0
  Clashscore            =   8.12
  RMS(bonds)            =   0.0088
  RMS(angles)           =   1.57
  MolProbity score      =   2.32

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  3.067)
  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:    8.335 (Z=  3.708)
  Mean delta:    1.666 (Z=  0.895)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   153.26    26.74  5.00e+00  2.86e+01   5.3*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   156.93    23.07  5.00e+00  2.13e+01   4.6*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   157.69    22.31  5.00e+00  1.99e+01   4.5*sigma

  Min. delta:    0.036
  Max. delta:   78.666
  Mean delta:   13.354

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002
  Max. delta:    0.194
  Mean delta:    0.079

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.072
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.451
    Angle     :  1.583   8.335   4079  Z= 0.681
    Chirality :  0.079   0.194    176
    Planarity :  0.009   0.054    327
    Dihedral  : 11.717  78.666    769
    Min Nonbonded Distance : 1.375
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  5.84 %
      Favored  : 89.78 %
    Rotamer:
      Outliers :  1.61 %
      Allowed  :  3.23 %
      Favored  : 95.16 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.11 (0.65), residues: 137
    helix: -0.68 (0.48), residues: 83
    sheet:  None (None), residues: 0
    loop : -0.56 (0.88), residues: 54
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.073   0.010   TYR A  50 
   ARG   0.055   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.012   0.003   PHE A  67 
   TYR   0.061   0.012   TYR A  50 
   ARG   0.008   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  92.70 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =  18.49
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.57
  MolProbity score      =   2.52

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: 0.73
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.80 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Ramachandran outliers =   4.38 %
                favored =  89.78 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.58
  MolProbity score      =   2.06

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 0
        1.23 -     1.42: 464
        1.42 -     1.61: 668
        1.61 -     1.81: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   THR A  83 "
       model="   0" pdb=" N   GLU A  84 "
    ideal  model  delta    sigma   weight residual
    1.329  1.350 -0.021 1.40e-02 5.10e+03 2.22e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.335 -0.014 1.00e-02 1.00e+04 1.99e+00
  bond model="   0" pdb=" C   TYR A  81 "
       model="   0" pdb=" N   THR A  82 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.48e+00
  bond model="   0" pdb=" C   GLY A  42 "
       model="   0" pdb=" N   HIS A  43 "
    ideal  model  delta    sigma   weight residual
    1.329  1.346 -0.017 1.40e-02 5.10e+03 1.47e+00
  bond model="   0" pdb=" CE1 HIS A 136 "
       model="   0" pdb=" NE2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.35e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.90 -   106.99: 133
      106.99 -   113.08: 2642
      113.08 -   119.17: 436
      119.17 -   125.26: 826
      125.26 -   131.35: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" CB  PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     109.00  114.12   -5.12 3.00e+00 1.11e-01 2.92e+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  104.27    4.73 3.00e+00 1.11e-01 2.48e+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  104.28    4.72 3.00e+00 1.11e-01 2.48e+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  104.35    4.65 3.00e+00 1.11e-01 2.41e+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  113.59   -4.59 3.00e+00 1.11e-01 2.34e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.55: 986
       15.55 -    31.10: 27
       31.10 -    46.66: 8
       46.66 -    62.21: 7
       62.21 -    77.76: 5
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
           model="   0" pdb=" CB  TYR A  91 "
           model="   0" pdb=" CG  TYR A  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.11   58.11     3      1.50e+01 4.44e-03 9.46e+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  -77.76   77.76     1      3.00e+01 1.11e-03 8.41e+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  -76.80   76.80     1      3.00e+01 1.11e-03 8.23e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 112
       0.032 -    0.064: 47
       0.064 -    0.096: 12
       0.096 -    0.128: 4
       0.128 -    0.160: 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    2.59   -0.16 2.00e-01 2.50e+01 6.38e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.11 2.00e-01 2.50e+01 3.22e-01
  chirality model="   0" pdb=" CA  ILE A 122 "
            model="   0" pdb=" N   ILE A 122 "
            model="   0" pdb=" C   ILE A 122 "
            model="   0" pdb=" CB  ILE A 122 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.54   -0.11 2.00e-01 2.50e+01 3.00e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.014 5.00e-02 4.00e+02   2.14e-02 7.32e-01
        model="   0" pdb=" N   PRO A   6 "   -0.037 5.00e-02 4.00e+02
        model="   0" pdb=" CA  PRO A   6 "    0.011 5.00e-02 4.00e+02
        model="   0" pdb=" CD  PRO A   6 "    0.012 5.00e-02 4.00e+02
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  HIS A 139 "    0.004 2.00e-02 2.50e+03   7.49e-03 5.60e-01
        model="   0" pdb=" C   HIS A 139 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" O   HIS A 139 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OXT HIS A 139 "    0.005 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.007 2.00e-02 2.50e+03   4.32e-03 5.60e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.008 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 "   -0.003 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 "    0.002 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 "   -0.002 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 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.007 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.09 -     1.79: 8
        1.79 -     2.49: 1584
        2.49 -     3.20: 6960
        3.20 -     3.90: 8269
        3.90 -     4.60: 13189
  Nonbonded interactions: 30010
  Sorted by model distance:
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" HE2 TYR A  91 "
     model   vdw
     1.089 2.100
  nonbonded model="   0" pdb=" OD2 ASP A 118 "
            model="   0" pdb="HH12 ARG A 127 "
     model   vdw
     1.542 1.850
  nonbonded model="   0" pdb="HD12 ILE A  86 "
            model="   0" pdb=" HD2 TYR A  89 "
     model   vdw
     1.554 2.270
  nonbonded model="   0" pdb="HD21 LEU A  93 "
            model="   0" pdb="HD13 LEU A  99 "
     model   vdw
     1.576 2.440
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.647 1.850
  ... (remaining 30005 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A TYR   12": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   16": "OE1" <-> "OE2"
    Residue "A GLU   24": "OE1" <-> "OE2"
    Residue "A GLU   32": "OE1" <-> "OE2"
    Residue "A GLU   49": "OE1" <-> "OE2"
    Residue "A GLU   55": "OE1" <-> "OE2"
    Residue "A PHE   67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   75": "OE1" <-> "OE2"
    Residue "A TYR   81": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU   84": "OE1" <-> "OE2"
    Residue "A TYR  105": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
    Residue "A GLU  120": "OE1" <-> "OE2"
    Residue "A GLU  123": "OE1" <-> "OE2"
    Residue "A GLU  133": "OE1" <-> "OE2"
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/usr/local/phenix-1.21.1-5286/modules/chem_data/mon_lib"
  Total number of atoms: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.012)
  Mean delta:    0.012 (Z=  0.604)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    5.956 (Z=  3.811)
  Mean delta:    1.552 (Z=  0.850)

                      ----------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   144.51    35.49  5.00e+00  5.04e+01   7.1*sigma
   A 115  ALA  CA
   A 115  ALA  C
   A 116  ASP  N
   A 116  ASP  CA        180.00   155.69    24.31  5.00e+00  2.36e+01   4.9*sigma
   A  81  TYR  CA
   A  81  TYR  C
   A  82  THR  N
   A  82  THR  CA        180.00   159.77    20.23  5.00e+00  1.64e+01   4.0*sigma

  Min. delta:    0.010
  Max. delta:   75.556
  Mean delta:   12.665

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.198
  Mean delta:    0.076

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.051
  Mean delta:    0.011

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.430
    Angle     :  1.510   5.956   4079  Z= 0.652
    Chirality :  0.076   0.198    176
    Planarity :  0.008   0.048    327
    Dihedral  : 12.051  84.001    769
    Min Nonbonded Distance : 1.418
  
  Molprobity Statistics.
    All-atom Clashscore : 12.17
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  1.46 %
      Favored  : 98.54 %
    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: -0.32 (0.68), residues: 137
    helix: -0.10 (0.50), residues: 87
    sheet:  None (None), residues: 0
    loop : -0.13 (0.94), residues: 50
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.024   0.006   PHE A  15 
   TYR   0.063   0.011   TYR A  50 
   ARG   0.044   0.011   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.014   0.005   PHE A  15 
   TYR   0.052   0.013   TYR A  50 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Ramachandran outliers =   0.00 %
                favored =  98.54 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =  12.17
  RMS(bonds)            =   0.0082
  RMS(angles)           =   1.51
  MolProbity score      =   1.76

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: 2218
  Number of models: 1
  Model: "   0"
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}
  Time building chain proxies: 1.05, per 1000 atoms: 0.47
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.303, 50.84, 66.449, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Time building chain proxies: 1.16, per 1000 atoms: 0.52
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (47.845, 44.107, 75.576, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  2.179)
  Mean delta:    0.007 (Z=  0.372)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    5.887 (Z=  3.271)
  Mean delta:    0.970 (Z=  0.500)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.006
  Max. delta:   87.368
  Mean delta:   12.475

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.164
  Mean delta:    0.051

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.039
  Mean delta:    0.005

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 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      :  0.005   0.022   2242  Z= 0.265
    Angle     :  1.196   5.887   4079  Z= 0.462
    Chirality :  0.051   0.164    176
    Planarity :  0.004   0.030    327
    Dihedral  : 11.262  87.368    769
    Min Nonbonded Distance : 1.533
  
  Molprobity Statistics.
    All-atom Clashscore : 8.57
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    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:  1.26 (0.72), residues: 137
    helix:  0.81 (0.65), residues: 57
    sheet:  1.37 (1.61), residues: 10
    loop :  1.00 (0.82), residues: 70
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.008   0.002   PHE A  67 
   TYR   0.025   0.005   TYR A  91 
   ARG   0.030   0.005   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 134 
   PHE   0.005   0.002   PHE A  67 
   TYR   0.020   0.005   TYR A  91 
   ARG   0.003   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.039 (Z=  2.979)
  Mean delta:    0.012 (Z=  0.634)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.36     4.24  1.00e+00  1.80e+01   4.2*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    6.198 (Z=  4.241)
  Mean delta:    1.585 (Z=  0.858)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A 138  HIS  CA
   A 138  HIS  C
   A 139  HIS  N
   A 139  HIS  CA        180.00   152.29    27.71  5.00e+00  3.07e+01   5.5*sigma
   A 137  HIS  CA
   A 137  HIS  C
   A 138  HIS  N
   A 138  HIS  CA        180.00   152.74    27.26  5.00e+00  2.97e+01   5.5*sigma
   A 136  HIS  CA
   A 136  HIS  C
   A 137  HIS  N
   A 137  HIS  CA        180.00   154.81    25.19  5.00e+00  2.54e+01   5.0*sigma
   A 135  HIS  CA
   A 135  HIS  C
   A 136  HIS  N
   A 136  HIS  CA        180.00   157.89    22.11  5.00e+00  1.96e+01   4.4*sigma

  Min. delta:    0.053
  Max. delta:   88.994
  Mean delta:   11.461

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.192
  Mean delta:    0.073

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  36  ASP  CB
   A  36  ASP  CG
   A  36  ASP  OD1
   A  36  ASP  OD2           0.051       0.088       25.71   4.4*sigma

  Min. delta:    0.000
  Max. delta:    0.051
  Mean delta:    0.010

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.039   2242  Z= 0.451
    Angle     :  1.531   6.198   4079  Z= 0.658
    Chirality :  0.073   0.192    176
    Planarity :  0.008   0.051    327
    Dihedral  : 10.526  88.994    769
    Min Nonbonded Distance : 1.514
  
  Molprobity Statistics.
    All-atom Clashscore : 7.21
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  2.92 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.31 (0.70), residues: 137
    helix:  0.21 (0.55), residues: 72
    sheet:  None (None), residues: 0
    loop :  0.43 (0.84), residues: 65
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.060   0.009   TYR A 111 
   ARG   0.035   0.009   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 137 
   PHE   0.011   0.004   PHE A  67 
   TYR   0.051   0.010   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 =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   8.57
  RMS(bonds)            =   0.0048
  RMS(angles)           =   1.20
  MolProbity score      =   1.77

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   7.21
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.53
  MolProbity score      =   1.70

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
        Number of residues, atoms: 139, 2218
          Classifications: {'peptide': 139}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 131}

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (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:    0.030 (Z=  2.149)
  Mean delta:    0.005 (Z=  0.313)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.974 (Z=  1.658)
  Mean delta:    0.562 (Z=  0.289)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   89.208
  Mean delta:   15.996

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.140
  Mean delta:    0.037

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.016
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.030   2242  Z= 0.223
    Angle     :  1.038   4.974   4079  Z= 0.371
    Chirality :  0.037   0.140    176
    Planarity :  0.002   0.015    327
    Dihedral  : 13.304  89.208    769
    Min Nonbonded Distance : 1.191
  
  Molprobity Statistics.
    All-atom Clashscore : 14.43
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  7.30 %
      Favored  : 92.70 %
    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: -1.41 (0.67), residues: 137
    helix: -0.90 (0.56), residues: 71
    sheet:  None (None), residues: 0
    loop : -0.83 (0.75), residues: 66
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.005   0.002   PHE A  45 
   TYR   0.011   0.002   TYR A  89 
   ARG   0.012   0.002   ARG A 129 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.004   0.001   PHE A  45 
   TYR   0.009   0.002   TYR A  89 
   ARG   0.003   0.001   ARG A 129 

                     ----------Asn/Gln/His flips----------                     

   A  28  GLN

=================================== Summary ===================================

  Time building chain proxies: 1.17, per 1000 atoms: 0.53
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (63.217, 59.512, 75.508, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  3.131)
  Mean delta:    0.012 (Z=  0.649)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.039 (Z=  3.866)
  Mean delta:    1.607 (Z=  0.870)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   141.73    38.27  5.00e+00  5.86e+01   7.7*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   157.55    22.45  5.00e+00  2.02e+01   4.5*sigma

  Min. delta:    0.014
  Max. delta:   89.242
  Mean delta:   13.312

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.224
  Mean delta:    0.081

                       ----------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   0.040   2242  Z= 0.462
    Angle     :  1.546   8.039   4079  Z= 0.666
    Chirality :  0.081   0.224    176
    Planarity :  0.008   0.038    327
    Dihedral  : 12.174  89.242    769
    Min Nonbonded Distance : 1.568
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  5.11 %
      Favored  : 94.16 %
    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 : 0.76 %
  
  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: -0.58 (0.70), residues: 137
    helix: -0.31 (0.51), residues: 85
    sheet:  None (None), residues: 0
    loop : -0.25 (0.97), residues: 52
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.060   0.008   TYR A 111 
   ARG   0.036   0.009   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.051   0.010   TYR A 111 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  92.70 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  14.43
  RMS(bonds)            =   0.0035
  RMS(angles)           =   1.04
  MolProbity score      =   2.13

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.07
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 1.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Time building chain proxies: 1.11, per 1000 atoms: 0.50
  Number of scatterers: 2218
  At special positions: 0
  Unit cell: (60.972, 56.353, 44.229, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       2     16.00
     O     217      8.00
     N     180      7.00
     C     713      6.00
     H    1106      1.00
    sf(0) = scattering factor at diffraction angle 0.
  Ramachandran outliers =   0.73 %
                favored =  94.16 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0087
  RMS(angles)           =   1.55
  MolProbity score      =   2.11

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.22: 0
        1.22 -     1.42: 464
        1.42 -     1.61: 668
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.336 -0.015 1.00e-02 1.00e+04 2.37e+00
  bond model="   0" pdb=" CE1 HIS A 135 "
       model="   0" pdb=" NE2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.321  1.334 -0.013 1.00e-02 1.00e+04 1.68e+00
  bond model="   0" pdb=" C   GLU A 120 "
       model="   0" pdb=" N   GLY A 121 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.49e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.332 -0.011 1.00e-02 1.00e+04 1.27e+00
  bond model="   0" pdb=" C   GLY A  87 "
       model="   0" pdb=" N   ASP A  88 "
    ideal  model  delta    sigma   weight residual
    1.329  1.314  0.015 1.40e-02 5.10e+03 1.13e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.28 -   106.45: 42
      106.45 -   112.63: 2736
      112.63 -   118.80: 433
      118.80 -   124.98: 826
      124.98 -   131.15: 42
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" N   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" C   PRO A  52 "
      ideal   model   delta    sigma   weight residual
     112.10  107.15    4.95 2.50e+00 1.60e-01 3.92e+00
  angle model="   0" pdb=" N   PRO A  52 "
        model="   0" pdb=" CA  PRO A  52 "
        model="   0" pdb=" HA  PRO A  52 "
      ideal   model   delta    sigma   weight residual
     110.00  115.04   -5.04 3.00e+00 1.11e-01 2.82e+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  104.33    4.67 3.00e+00 1.11e-01 2.42e+00
  angle model="   0" pdb=" CB  PRO A 117 "
        model="   0" pdb=" CA  PRO A 117 "
        model="   0" pdb=" HA  PRO A 117 "
      ideal   model   delta    sigma   weight residual
     109.00  113.60   -4.60 3.00e+00 1.11e-01 2.36e+00
  angle model="   0" pdb=" O   HIS A 139 "
        model="   0" pdb=" C   HIS A 139 "
        model="   0" pdb=" OXT HIS A 139 "
      ideal   model   delta    sigma   weight residual
     118.00  122.57   -4.57 3.00e+00 1.11e-01 2.32e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.52: 982
       13.52 -    27.04: 25
       27.04 -    40.56: 18
       40.56 -    54.08: 7
       54.08 -    67.61: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLN A  66 "
           model="   0" pdb=" CG  GLN A  66 "
           model="   0" pdb=" CD  GLN A  66 "
           model="   0" pdb=" OE1 GLN A  66 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   67.61  -67.61     2      3.00e+01 1.11e-03 4.56e+00
  dihedral model="   0" pdb=" CA  ILE A  51 "
           model="   0" pdb=" C   ILE A  51 "
           model="   0" pdb=" N   PRO A  52 "
           model="   0" pdb=" CA  PRO A  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  170.05    9.95     0      5.00e+00 4.00e-02 3.96e+00
  dihedral model="   0" pdb=" CA  ASP A  36 "
           model="   0" pdb=" CB  ASP A  36 "
           model="   0" pdb=" CG  ASP A  36 "
           model="   0" pdb=" OD1 ASP A  36 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   32.74  -32.74     1      2.00e+01 2.50e-03 3.81e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.029: 122
       0.029 -    0.058: 36
       0.058 -    0.086: 9
       0.086 -    0.115: 5
       0.115 -    0.143: 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    2.58   -0.14 2.00e-01 2.50e+01 5.13e-01
  chirality model="   0" pdb=" CA  ILE A   4 "
            model="   0" pdb=" N   ILE A   4 "
            model="   0" pdb=" C   ILE A   4 "
            model="   0" pdb=" CB  ILE A   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  chirality model="   0" pdb=" CA  ILE A 131 "
            model="   0" pdb=" N   ILE A 131 "
            model="   0" pdb=" C   ILE A 131 "
            model="   0" pdb=" CB  ILE A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.71e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" C   THR A   5 "    0.014 5.00e-02 4.00e+02   2.18e-02 7.60e-01
        model="   0" pdb=" N   PRO A   6 "   -0.038 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  HIS A 139 "    0.008 2.00e-02 2.50e+03   5.05e-03 5.10e-01
        model="   0" pdb=" CG  HIS A 139 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 139 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 139 "   -0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 139 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 139 "    0.004 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  HIS A 136 "    0.004 2.00e-02 2.50e+03   4.93e-03 4.86e-01
        model="   0" pdb=" CG  HIS A 136 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" ND1 HIS A 136 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 HIS A 136 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 HIS A 136 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" NE2 HIS A 136 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 HIS A 136 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 HIS A 136 "    0.006 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.11: 75
        2.11 -     2.74: 4150
        2.74 -     3.36: 6067
        3.36 -     3.98: 7684
        3.98 -     4.60: 11851
  Nonbonded interactions: 29827
  Sorted by model distance:
  nonbonded model="   0" pdb="HD23 LEU A  93 "
            model="   0" pdb=" H   SER A  98 "
     model   vdw
     1.493 2.270
  nonbonded model="   0" pdb="HG22 ILE A  77 "
            model="   0" pdb="HD11 LEU A  93 "
     model   vdw
     1.549 2.440
  nonbonded model="   0" pdb="HD12 LEU A 132 "
            model="   0" pdb=" HD2 HIS A 137 "
     model   vdw
     1.616 2.270
  nonbonded model="   0" pdb=" HB2 LEU A 119 "
            model="   0" pdb=" HD2 ARG A 127 "
     model   vdw
     1.715 2.440
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.724 1.850
  ... (remaining 29822 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: 97
        1.23 -     1.43: 375
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.66e+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 6.12e+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 5.78e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.380 -0.026 1.10e-02 8.26e+03 5.68e+00
  bond model="   0" pdb=" CE1 HIS A 138 "
       model="   0" pdb=" NE2 HIS A 138 "
    ideal  model  delta    sigma   weight residual
    1.321  1.345 -0.024 1.00e-02 1.00e+04 5.54e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.25 -   105.97: 79
      105.97 -   111.69: 2465
      111.69 -   117.41: 514
      117.41 -   123.13: 805
      123.13 -   128.85: 216
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.57    4.03 1.00e+00 1.00e+00 1.62e+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 136 "
        model="   0" pdb=" CG  HIS A 136 "
        model="   0" pdb=" CD2 HIS A 136 "
      ideal   model   delta    sigma   weight residual
     131.20  126.55    4.65 1.30e+00 5.92e-01 1.28e+01
  angle model="   0" pdb=" 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 1.27e+01
  angle model="   0" pdb=" C   THR A  82 "
        model="   0" pdb=" N   THR A  83 "
        model="   0" pdb=" CA  THR A  83 "
      ideal   model   delta    sigma   weight residual
     121.70  128.02   -6.32 1.80e+00 3.09e-01 1.23e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 965
       17.08 -    34.15: 47
       34.15 -    51.23: 14
       51.23 -    68.30: 6
       68.30 -    85.38: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.54   21.46     0      5.00e+00 4.00e-02 1.84e+01
  dihedral model="   0" pdb=" CA  PRO A 114 "
           model="   0" pdb=" C   PRO A 114 "
           model="   0" pdb=" N   ALA A 115 "
           model="   0" pdb=" CA  ALA A 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.30   15.70     0      5.00e+00 4.00e-02 9.86e+00
  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  164.64   15.36     0      5.00e+00 4.00e-02 9.43e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 80
       0.049 -    0.099: 58
       0.099 -    0.148: 30
       0.148 -    0.197: 6
       0.197 -    0.246: 2
  Chirality restraints: 176
  Sorted by residual:
  chirality model="   0" pdb=" CB  THR A  92 "
            model="   0" pdb=" CA  THR A  92 "
            model="   0" pdb=" OG1 THR A  92 "
            model="   0" pdb=" CG2 THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality model="   0" pdb=" CA  THR A  92 "
            model="   0" pdb=" N   THR A  92 "
            model="   0" pdb=" C   THR A  92 "
            model="   0" pdb=" CB  THR A  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.30    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality model="   0" pdb=" CA  PHE A  45 "
            model="   0" pdb=" N   PHE A  45 "
            model="   0" pdb=" C   PHE A  45 "
            model="   0" pdb=" CB  PHE A  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.39e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  81 "    0.352 2.00e-02 2.50e+03   1.49e-01 6.67e+02
        model="   0" pdb=" CG  TYR A  81 "   -0.023 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  81 "   -0.081 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  81 "   -0.067 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  81 "   -0.039 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  81 "   -0.052 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  81 "    0.027 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  81 "    0.286 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  81 "   -0.147 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  81 "   -0.107 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  81 "   -0.055 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  81 "   -0.093 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   3.32e-02 3.30e+01
        model="   0" pdb=" CG  TYR A  50 "    0.002 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "   -0.069 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "    0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "    0.025 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.021 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 "    0.056 2.00e-02 2.50e+03   2.20e-02 1.46e+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 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.003 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "    0.037 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.67 -     2.25: 245
        2.25 -     2.84: 4864
        2.84 -     3.43: 5739
        3.43 -     4.01: 7286
        4.01 -     4.60: 10850
  Nonbonded interactions: 28984
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD1 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.668 1.850
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.668 1.850
  nonbonded model="   0" pdb="HD11 ILE A  77 "
            model="   0" pdb="HD23 LEU A  93 "
     model   vdw
     1.695 2.440
  nonbonded model="   0" pdb=" OH  TYR A  81 "
            model="   0" pdb=" HG1 THR A  92 "
     model   vdw
     1.702 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  95 "
            model="   0" pdb=" HG  SER A  97 "
     model   vdw
     1.728 1.850
  ... (remaining 28979 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  2.882)
  Mean delta:    0.012 (Z=  0.638)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  95  ASP  CA
   A  95  ASP  CB
   A  95  ASP  CG        112.60   117.96    -5.36  1.00e+00  2.87e+01   5.4*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.424 (Z=  5.359)
  Mean delta:    1.576 (Z=  0.861)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.020
  Max. delta:   81.930
  Mean delta:   11.929

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.222
  Mean delta:    0.081

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.043
  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   2242  Z= 0.454
    Angle     :  1.532   6.529   4079  Z= 0.661
    Chirality :  0.081   0.222    176
    Planarity :  0.008   0.036    327
    Dihedral  : 11.295  84.036    769
    Min Nonbonded Distance : 1.495
  
  Molprobity Statistics.
    All-atom Clashscore : 17.13
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    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: -0.09 (0.68), residues: 137
    helix:  0.29 (0.51), residues: 84
    sheet:  None (None), residues: 0
    loop : -0.46 (0.89), residues: 53
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 139 
   PHE   0.016   0.005   PHE A  15 
   TYR   0.081   0.012   TYR A  81 
   ARG   0.036   0.008   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   0.066   0.014   TYR A  81 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.549)
  Mean delta:    0.012 (Z=  0.614)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        121.70   129.53    -7.83  1.80e+00  1.89e+01   4.3*sigma

  Min. delta:    0.002 (Z=  0.001)
  Max. delta:    7.825 (Z=  4.347)
  Mean delta:    1.621 (Z=  0.885)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   157.59    22.41  5.00e+00  2.01e+01   4.5*sigma

  Min. delta:    0.031
  Max. delta:   85.768
  Mean delta:   12.178

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.211
  Mean delta:    0.077

                       ----------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            0.058       0.105       66.76   5.3*sigma

  Min. delta:    0.000
  Max. delta:    0.060
  Mean delta:    0.013

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.437
    Angle     :  1.555   7.825   4079  Z= 0.674
    Chirality :  0.077   0.211    176
    Planarity :  0.010   0.056    327
    Dihedral  : 11.531  85.768    769
    Min Nonbonded Distance : 1.601
  
  Molprobity Statistics.
    All-atom Clashscore : 11.72
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  4.38 %
      Favored  : 94.16 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.81 %
      Favored  : 98.39 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.21 (0.69), residues: 137
    helix:  0.24 (0.52), residues: 78
    sheet:  None (None), residues: 0
    loop :  0.22 (0.89), residues: 59
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.036   0.007   PHE A  67 
   TYR   0.128   0.020   TYR A  89 
   ARG   0.049   0.013   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A  43 
   PHE   0.022   0.007   PHE A  67 
   TYR   0.105   0.024   TYR A  81 
   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: 1.19 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  17.13
  RMS(bonds)            =   0.0086
  RMS(angles)           =   1.53
  MolProbity score      =   1.78

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   1.46 %
                favored =  94.16 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  11.72
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.56
  MolProbity score      =   1.98

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 124
        1.23 -     1.43: 348
        1.43 -     1.63: 660
        1.63 -     1.83: 4
  Bond restraints: 2242
  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  1.347 -0.026 1.00e-02 1.00e+04 6.69e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.347 -0.026 1.00e-02 1.00e+04 6.63e+00
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.379 -0.025 1.10e-02 8.26e+03 5.32e+00
  bond model="   0" pdb=" CZ  ARG A 129 "
       model="   0" pdb=" NH2 ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.330  1.300  0.030 1.30e-02 5.92e+03 5.25e+00
  bond model="   0" pdb=" CG  HIS A 137 "
       model="   0" pdb=" CD2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.354  1.379 -0.025 1.10e-02 8.26e+03 5.19e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.24 -   106.01: 93
      106.01 -   111.79: 2489
      111.79 -   117.56: 486
      117.56 -   123.34: 837
      123.34 -   129.11: 174
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" OE1 GLN A  28 "
        model="   0" pdb=" CD  GLN A  28 "
        model="   0" pdb=" NE2 GLN A  28 "
      ideal   model   delta    sigma   weight residual
     122.60  118.61    3.99 1.00e+00 1.00e+00 1.59e+01
  angle model="   0" pdb=" CA  ASP A  36 "
        model="   0" pdb=" CB  ASP A  36 "
        model="   0" pdb=" CG  ASP A  36 "
      ideal   model   delta    sigma   weight residual
     112.60  116.57   -3.97 1.00e+00 1.00e+00 1.58e+01
  angle model="   0" pdb=" C   ASP A  88 "
        model="   0" pdb=" N   TYR A  89 "
        model="   0" pdb=" CA  TYR A  89 "
      ideal   model   delta    sigma   weight residual
     121.70  128.54   -6.84 1.80e+00 3.09e-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  118.86    3.74 1.00e+00 1.00e+00 1.40e+01
  angle model="   0" pdb=" CA  ASP A  29 "
        model="   0" pdb=" CB  ASP A  29 "
        model="   0" pdb=" CG  ASP A  29 "
      ideal   model   delta    sigma   weight residual
     112.60  116.23   -3.63 1.00e+00 1.00e+00 1.31e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 963
       17.44 -    34.89: 50
       34.89 -    52.33: 13
       52.33 -    69.77: 6
       69.77 -    87.21: 1
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  ILE A  86 "
           model="   0" pdb=" C   ILE A  86 "
           model="   0" pdb=" N   GLY A  87 "
           model="   0" pdb=" CA  GLY A  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.83  -26.17     0      5.00e+00 4.00e-02 2.74e+01
  dihedral model="   0" pdb=" CA  LEU A  93 "
           model="   0" pdb=" C   LEU A  93 "
           model="   0" pdb=" N   GLY A  94 "
           model="   0" pdb=" CA  GLY A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.66   21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.70   17.30     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.040: 65
       0.040 -    0.079: 45
       0.079 -    0.119: 35
       0.119 -    0.158: 24
       0.158 -    0.198: 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 9.75e-01
  chirality model="   0" pdb=" CB  THR A  82 "
            model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" OG1 THR A  82 "
            model="   0" pdb=" CG2 THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.36    0.20 2.00e-01 2.50e+01 9.64e-01
  chirality model="   0" pdb=" CA  ASP A  88 "
            model="   0" pdb=" N   ASP A  88 "
            model="   0" pdb=" C   ASP A  88 "
            model="   0" pdb=" CB  ASP A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.84e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.081 2.00e-02 2.50e+03   3.54e-02 3.77e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.016 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.017 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.011 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.072 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.026 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.030 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "   -0.022 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "   -0.018 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  ASP A  36 "   -0.021 2.00e-02 2.50e+03   4.39e-02 1.93e+01
        model="   0" pdb=" CG  ASP A  36 "    0.076 2.00e-02 2.50e+03
        model="   0" pdb=" OD1 ASP A  36 "   -0.028 2.00e-02 2.50e+03
        model="   0" pdb=" OD2 ASP A  36 "   -0.026 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   2.08e-02 1.30e+01
        model="   0" pdb=" CG  TYR A 111 "    0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "    0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "    0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A 111 "   -0.034 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A 111 "    0.014 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 "    0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.004 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.15: 101
        2.15 -     2.76: 3975
        2.76 -     3.37: 6161
        3.37 -     3.99: 7213
        3.99 -     4.60: 10937
  Nonbonded interactions: 28387
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HH  TYR A  68 "
     model   vdw
     1.533 1.850
  nonbonded model="   0" pdb="HG23 ILE A  78 "
            model="   0" pdb=" HA  SER A  97 "
     model   vdw
     1.742 2.440
  nonbonded model="   0" pdb=" OE2 GLU A  24 "
            model="   0" pdb=" HZ2 LYS A  27 "
     model   vdw
     1.759 1.850
  nonbonded model="   0" pdb=" O   LYS A  79 "
            model="   0" pdb=" HG1 THR A  82 "
     model   vdw
     1.783 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.784 1.850
  ... (remaining 28382 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.041 (Z=  2.467)
  Mean delta:    0.012 (Z=  0.622)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    6.474 (Z=  3.998)
  Mean delta:    1.577 (Z=  0.854)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   156.91    23.09  5.00e+00  2.13e+01   4.6*sigma
   A  82  THR  CA
   A  82  THR  C
   A  83  THR  N
   A  83  THR  CA        180.00   158.72    21.28  5.00e+00  1.81e+01   4.3*sigma

  Min. delta:    0.019
  Max. delta:   89.195
  Mean delta:   13.138

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.239
  Mean delta:    0.079

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.075
  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   2242  Z= 0.443
    Angle     :  1.529   6.474   4079  Z= 0.657
    Chirality :  0.079   0.239    176
    Planarity :  0.009   0.056    327
    Dihedral  : 11.714  89.195    769
    Min Nonbonded Distance : 1.481
  
  Molprobity Statistics.
    All-atom Clashscore : 7.66
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  2.19 %
      Favored  : 97.81 %
    Rotamer:
      Outliers :  2.42 %
      Allowed  :  4.03 %
      Favored  : 93.55 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.12 (0.67), residues: 137
    helix:  0.05 (0.48), residues: 88
    sheet:  None (None), residues: 0
    loop : -0.03 (0.95), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.070   0.010   TYR A  50 
   ARG   0.061   0.014   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.058   0.012   TYR A  50 
   ARG   0.006   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.73
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  264

  Time building geometry restraints manager: 0.87 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.949)
  Mean delta:    0.012 (Z=  0.678)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  80  GLY  CA
   A  80  GLY  C
   A  81  TYR  N         116.20   124.58    -8.38  2.00e+00  1.75e+01   4.2*sigma
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.51     4.09  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:   10.906 (Z=  4.188)
  Mean delta:    1.666 (Z=  0.898)

                      ----------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  -151.88   -28.12  5.00e+00  3.16e+01   5.6*sigma
   A  76  SER  CA
   A  76  SER  C
   A  77  ILE  N
   A  77  ILE  CA        180.00   157.94    22.06  5.00e+00  1.95e+01   4.4*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00  -158.92   -21.08  5.00e+00  1.78e+01   4.2*sigma

  Min. delta:    0.005
  Max. delta:   89.542
  Mean delta:   13.064

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.273
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.057
  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   2242  Z= 0.483
    Angle     :  1.573  10.906   4079  Z= 0.681
    Chirality :  0.082   0.273    176
    Planarity :  0.008   0.048    327
    Dihedral  : 11.620  89.542    769
    Min Nonbonded Distance : 1.620
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  3.65 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  4.03 %
      Allowed  :  1.61 %
      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:  0.29 (0.72), residues: 137
    helix:  0.63 (0.53), residues: 81
    sheet:  None (None), residues: 0
    loop : -0.31 (0.95), residues: 56
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 136 
   PHE   0.058   0.010   PHE A  15 
   TYR   0.065   0.009   TYR A  50 
   ARG   0.046   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 136 
   PHE   0.037   0.010   PHE A  15 
   TYR   0.054   0.011   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  97.81 %
  Rotamer outliers      =   2.42 %
  C-beta deviations     =     0
  Clashscore            =   7.66
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.53
  MolProbity score      =   1.75

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.04: 1106
        1.04 -     1.23: 86
        1.23 -     1.43: 386
        1.43 -     1.62: 660
        1.62 -     1.82: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" CG  HIS A 136 "
       model="   0" pdb=" CD2 HIS A 136 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 7.17e+00
  bond model="   0" pdb=" CG  HIS A 135 "
       model="   0" pdb=" CD2 HIS A 135 "
    ideal  model  delta    sigma   weight residual
    1.354  1.383 -0.029 1.10e-02 8.26e+03 6.80e+00
  bond model="   0" pdb=" CG  HIS A 134 "
       model="   0" pdb=" CD2 HIS A 134 "
    ideal  model  delta    sigma   weight residual
    1.354  1.382 -0.028 1.10e-02 8.26e+03 6.60e+00
  bond model="   0" pdb=" ND1 HIS A 139 "
       model="   0" pdb=" CE1 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.321  1.346 -0.025 1.00e-02 1.00e+04 6.15e+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 2237 not shown)

  Histogram of bond angle deviations from ideal:
      101.77 -   107.42: 436
      107.42 -   113.07: 2329
      113.07 -   118.71: 421
      118.71 -   124.36: 811
      124.36 -   130.01: 82
  Bond angle restraints: 4079
  Sorted by residual:
  angle model="   0" pdb=" C   GLY A  87 "
        model="   0" pdb=" N   ASP A  88 "
        model="   0" pdb=" CA  ASP A  88 "
      ideal   model   delta    sigma   weight residual
     121.70  130.01   -8.31 1.80e+00 3.09e-01 2.13e+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  118.62    3.98 1.00e+00 1.00e+00 1.59e+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  126.14    5.06 1.30e+00 5.92e-01 1.51e+01
  angle model="   0" pdb=" CB  HIS A 134 "
        model="   0" pdb=" CG  HIS A 134 "
        model="   0" pdb=" CD2 HIS A 134 "
      ideal   model   delta    sigma   weight residual
     131.20  126.37    4.83 1.30e+00 5.92e-01 1.38e+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  126.51    4.69 1.30e+00 5.92e-01 1.30e+01
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.40: 963
       17.40 -    34.80: 50
       34.80 -    52.21: 15
       52.21 -    69.61: 3
       69.61 -    87.01: 2
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CA  TYR A  81 "
           model="   0" pdb=" C   TYR A  81 "
           model="   0" pdb=" N   THR A  82 "
           model="   0" pdb=" CA  THR A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.24   35.76     0      5.00e+00 4.00e-02 5.12e+01
  dihedral model="   0" pdb=" CA  THR A  92 "
           model="   0" pdb=" C   THR A  92 "
           model="   0" pdb=" N   LEU A  93 "
           model="   0" pdb=" CA  LEU A  93 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.95   30.05     0      5.00e+00 4.00e-02 3.61e+01
  dihedral model="   0" pdb=" CA  SER A  90 "
           model="   0" pdb=" C   SER A  90 "
           model="   0" pdb=" N   TYR A  91 "
           model="   0" pdb=" CA  TYR A  91 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.43   29.57     0      5.00e+00 4.00e-02 3.50e+01
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.037: 71
       0.037 -    0.073: 33
       0.073 -    0.109: 38
       0.109 -    0.145: 28
       0.145 -    0.181: 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 8.18e-01
  chirality model="   0" pdb=" CA  THR A  82 "
            model="   0" pdb=" N   THR A  82 "
            model="   0" pdb=" C   THR A  82 "
            model="   0" pdb=" CB  THR A  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.71   -0.18 2.00e-01 2.50e+01 8.10e-01
  chirality model="   0" pdb=" CA  LEU A  93 "
            model="   0" pdb=" N   LEU A  93 "
            model="   0" pdb=" C   LEU A  93 "
            model="   0" pdb=" CB  LEU A  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 6.85e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.068 2.00e-02 2.50e+03   2.91e-02 2.54e+01
        model="   0" pdb=" CG  TYR A  50 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.010 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.005 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.058 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 "   -0.025 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 "   -0.014 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   2.20e-02 1.45e+01
        model="   0" pdb=" CG  TYR A 111 "   -0.015 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A 111 "   -0.012 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A 111 "   -0.014 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A 111 "   -0.006 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A 111 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A 111 "    0.004 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 "   -0.013 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.021 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "   -0.002 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CA  LEU A  93 "   -0.015 2.00e-02 2.50e+03   3.02e-02 9.10e+00
        model="   0" pdb=" C   LEU A  93 "    0.052 2.00e-02 2.50e+03
        model="   0" pdb=" O   LEU A  93 "   -0.020 2.00e-02 2.50e+03
        model="   0" pdb=" N   GLY A  94 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.07 -     1.77: 6
        1.77 -     2.48: 1464
        2.48 -     3.19: 6734
        3.19 -     3.89: 7950
        3.89 -     4.60: 12068
  Nonbonded interactions: 28222
  Sorted by model distance:
  nonbonded model="   0" pdb=" HB3 LYS A  79 "
            model="   0" pdb=" HD1 TYR A  81 "
     model   vdw
     1.066 2.270
  nonbonded model="   0" pdb=" HZ1 LYS A  10 "
            model="   0" pdb=" OD1 ASP A  23 "
     model   vdw
     1.617 1.850
  nonbonded model="   0" pdb="HG22 ILE A  86 "
            model="   0" pdb=" H   GLY A  87 "
     model   vdw
     1.631 2.270
  nonbonded model="   0" pdb=" OD2 ASP A  36 "
            model="   0" pdb=" HZ1 LYS A 101 "
     model   vdw
     1.732 1.850
  nonbonded model="   0" pdb=" OD1 ASP A  44 "
            model="   0" pdb=" HG  SER A  46 "
     model   vdw
     1.735 1.850
  ... (remaining 28217 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
  Ramachandran outliers =   0.73 %
                favored =  95.62 %
  Rotamer outliers      =   4.03 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.57
  MolProbity score      =   2.14

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.041 (Z=  2.964)
  Mean delta:    0.012 (Z=  0.630)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.43     4.17  1.00e+00  1.74e+01   4.2*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.559 (Z=  4.167)
  Mean delta:    1.566 (Z=  0.840)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   159.94    20.06  5.00e+00  1.61e+01   4.0*sigma

  Min. delta:    0.024
  Max. delta:   89.994
  Mean delta:   11.772

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.182
  Mean delta:    0.074

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.061
  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   2242  Z= 0.449
    Angle     :  1.521   6.559   4079  Z= 0.648
    Chirality :  0.074   0.182    176
    Planarity :  0.008   0.046    327
    Dihedral  : 11.321  89.994    769
    Min Nonbonded Distance : 1.578
  
  Molprobity Statistics.
    All-atom Clashscore : 6.31
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  3.65 %
      Favored  : 96.35 %
    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: -0.20 (0.68), residues: 137
    helix:  0.38 (0.51), residues: 88
    sheet:  None (None), residues: 0
    loop : -0.92 (0.89), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.024   0.006   PHE A  15 
   TYR   0.074   0.010   TYR A  50 
   ARG   0.049   0.012   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.015   0.007   PHE A  15 
   TYR   0.060   0.012   TYR A  50 
   ARG   0.005   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


  Number of disulfides: simple=0, symmetry=0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0
  Custom bonds:
    Warning: Ignoring bond with distance_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
    Total number of added/changed bonds: 0
  Custom angles:
    Warning: Ignoring angle with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
    Total number of new custom angles: 0
    Total number of changed angles: 0
  Custom dihedrals:
    Warning: Ignoring dihedral with angle_ideal = None:
      atom_selection_1 = None
      atom_selection_2 = None
      atom_selection_3 = None
      atom_selection_4 = None
    Total number of custom dihedrals: 0
  Custom planarities:
    Warning: Ignoring planarity with with sigma <= 0:
    Total number of custom planarities: 0
  Custom parallelities:
    Warning: Ignoring parallelity with empty atom selection.
    Total number of custom parallelities: 0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.04
  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.

  Ramachandran outliers =   0.00 %
                favored =  96.35 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   6.31
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.52
  MolProbity score      =   1.59

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Histogram of bond lengths:
        0.84 -     1.03: 1106
        1.03 -     1.23: 3
        1.23 -     1.42: 460
        1.42 -     1.61: 669
        1.61 -     1.80: 4
  Bond restraints: 2242
  Sorted by residual:
  bond model="   0" pdb=" C   VAL A 126 "
       model="   0" pdb=" N   ARG A 127 "
    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=" CD2 HIS A 139 "
       model="   0" pdb=" NE2 HIS A 139 "
    ideal  model  delta    sigma   weight residual
    1.374  1.389 -0.015 1.10e-02 8.26e+03 1.88e+00
  bond model="   0" pdb=" C   ARG A 127 "
       model="   0" pdb=" N   MET A 128 "
    ideal  model  delta    sigma   weight residual
    1.329  1.312  0.017 1.40e-02 5.10e+03 1.53e+00
  bond model="   0" pdb=" ND1 HIS A 137 "
       model="   0" pdb=" CE1 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.309  0.012 1.00e-02 1.00e+04 1.51e+00
  bond model="   0" pdb=" CE1 HIS A 137 "
       model="   0" pdb=" NE2 HIS A 137 "
    ideal  model  delta    sigma   weight residual
    1.321  1.333 -0.012 1.00e-02 1.00e+04 1.45e+00
  ... (remaining 2237 not shown)

  Histogram of bond angle deviations from ideal:
      100.28 -   106.50: 55
      106.50 -   112.72: 2700
      112.72 -   118.94: 452
      118.94 -   125.16: 829
      125.16 -   131.37: 43
  Bond angle restraints: 4079
  Sorted by residual:
  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  105.14    4.86 3.00e+00 1.11e-01 2.62e+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  104.15    4.85 3.00e+00 1.11e-01 2.61e+00
  angle model="   0" pdb=" C   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" CB  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     111.60  108.37    3.23 2.00e+00 2.50e-01 2.61e+00
  angle model="   0" pdb=" N   ILE A 108 "
        model="   0" pdb=" CA  ILE A 108 "
        model="   0" pdb=" HA  ILE A 108 "
      ideal   model   delta    sigma   weight residual
     110.00  105.35    4.65 3.00e+00 1.11e-01 2.41e+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  113.56   -4.56 3.00e+00 1.11e-01 2.31e+00
  ... (remaining 4074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.12: 978
       17.12 -    34.24: 27
       34.24 -    51.35: 12
       51.35 -    68.47: 8
       68.47 -    85.59: 8
  Dihedral angle restraints: 1033
    sinusoidal: 562
      harmonic: 471
  Sorted by residual:
  dihedral model="   0" pdb=" CB  GLU A  55 "
           model="   0" pdb=" CG  GLU A  55 "
           model="   0" pdb=" CD  GLU A  55 "
           model="   0" pdb=" OE1 GLU A  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.59  -85.59     1      3.00e+01 1.11e-03 9.85e+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  -78.08   78.08     1      3.00e+01 1.11e-03 8.46e+00
  dihedral model="   0" pdb=" CB  GLU A  75 "
           model="   0" pdb=" CG  GLU A  75 "
           model="   0" pdb=" CD  GLU A  75 "
           model="   0" pdb=" OE1 GLU A  75 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   76.67  -76.67     1      3.00e+01 1.11e-03 8.21e+00
  ... (remaining 1030 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 105
       0.034 -    0.067: 51
       0.067 -    0.100: 9
       0.100 -    0.134: 8
       0.134 -    0.167: 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    2.60   -0.17 2.00e-01 2.50e+01 6.97e-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 6.10e-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    2.59   -0.15 2.00e-01 2.50e+01 5.95e-01
  ... (remaining 173 not shown)

  Planarity restraints: 327
  Sorted by residual:
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  50 "    0.018 2.00e-02 2.50e+03   6.78e-03 1.38e+00
        model="   0" pdb=" CG  TYR A  50 "   -0.008 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  50 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" CE1 TYR A  50 "   -0.001 2.00e-02 2.50e+03
        model="   0" pdb=" CE2 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" CZ  TYR A  50 "    0.001 2.00e-02 2.50e+03
        model="   0" pdb=" OH  TYR A  50 "    0.006 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  50 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  50 "   -0.007 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A  50 "    0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A  50 "    0.003 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A  12 "    0.015 2.00e-02 2.50e+03   5.87e-03 1.04e+00
        model="   0" pdb=" CG  TYR A  12 "   -0.004 2.00e-02 2.50e+03
        model="   0" pdb=" CD1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" CD2 TYR A  12 "   -0.004 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 "   -0.000 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 "    0.009 2.00e-02 2.50e+03
        model="   0" pdb=" HD1 TYR A  12 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A  12 "   -0.007 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 "    0.000 2.00e-02 2.50e+03
                                              delta    sigma   weight rms_deltas residual
  plane model="   0" pdb=" CB  TYR A 111 "    0.014 2.00e-02 2.50e+03   5.44e-03 8.88e-01
        model="   0" pdb=" CG  TYR A 111 "   -0.007 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 "    0.002 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 "   -0.000 2.00e-02 2.50e+03
        model="   0" pdb=" HD2 TYR A 111 "   -0.005 2.00e-02 2.50e+03
        model="   0" pdb=" HE1 TYR A 111 "   -0.003 2.00e-02 2.50e+03
        model="   0" pdb=" HE2 TYR A 111 "    0.002 2.00e-02 2.50e+03
  ... (remaining 324 not shown)

  Histogram of nonbonded interaction distances:
        1.47 -     2.10: 78
        2.10 -     2.72: 3995
        2.72 -     3.35: 6177
        3.35 -     3.97: 7742
        3.97 -     4.60: 11966
  Nonbonded interactions: 29958
  Sorted by model distance:
  nonbonded model="   0" pdb=" OD2 ASP A  74 "
            model="   0" pdb=" HG  SER A  76 "
     model   vdw
     1.474 1.850
  nonbonded model="   0" pdb="HG22 ILE A  71 "
            model="   0" pdb="HD11 ILE A  78 "
     model   vdw
     1.576 2.440
  nonbonded model="   0" pdb="HE21 GLN A  66 "
            model="   0" pdb=" OH  TYR A  89 "
     model   vdw
     1.628 1.850
  nonbonded model="   0" pdb=" O   VAL A  41 "
            model="   0" pdb=" H   LYS A 113 "
     model   vdw
     1.686 1.850
  nonbonded model="   0" pdb=" HE  ARG A  21 "
            model="   0" pdb=" OD2 ASP A  29 "
     model   vdw
     1.729 1.850
  ... (remaining 29953 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.039 (Z=  2.953)
  Mean delta:    0.012 (Z=  0.617)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.56     4.04  1.00e+00  1.63e+01   4.0*sigma

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.467 (Z=  4.036)
  Mean delta:    1.575 (Z=  0.866)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.007
  Max. delta:   86.914
  Mean delta:   12.552

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.195
  Mean delta:    0.073

                       ----------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   0.039   2242  Z= 0.440
    Angle     :  1.527   6.467   4079  Z= 0.662
    Chirality :  0.073   0.195    176
    Planarity :  0.007   0.032    327
    Dihedral  : 11.095  86.914    769
    Min Nonbonded Distance : 1.636
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  0.00 %
      Favored  : 99.27 %
    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:  0.34 (0.69), residues: 137
    helix: -0.37 (0.52), residues: 76
    sheet: -2.10 (0.96), residues: 12
    loop :  2.42 (0.96), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.052   0.009   TYR A  12 
   ARG   0.034   0.010   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.014   0.004   PHE A  67 
   TYR   0.043   0.010   TYR A  12 
   ARG   0.004   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  99.27 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.53
  MolProbity score      =   1.42

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.735)
  Mean delta:    0.013 (Z=  0.671)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.52     4.08  1.00e+00  1.67e+01   4.1*sigma

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.710 (Z=  4.083)
  Mean delta:    1.673 (Z=  0.914)

                      ----------Dihedral angles----------                      

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   125.96    54.04  5.00e+00  1.17e+02  10.8*sigma
   A  91  TYR  CA
   A  91  TYR  C
   A  92  THR  N
   A  92  THR  CA        180.00   140.41    39.59  5.00e+00  6.27e+01   7.9*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   143.94    36.06  5.00e+00  5.20e+01   7.2*sigma
   A  88  ASP  CA
   A  88  ASP  C
   A  89  TYR  N
   A  89  TYR  CA        180.00   158.35    21.65  5.00e+00  1.88e+01   4.3*sigma

  Min. delta:    0.029
  Max. delta:   85.429
  Mean delta:   12.983

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.185
  Mean delta:    0.079

                       ----------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      :  0.009   0.040   2242  Z= 0.478
    Angle     :  1.582   7.461   4079  Z= 0.690
    Chirality :  0.079   0.185    176
    Planarity :  0.008   0.041    327
    Dihedral  : 11.331  85.429    769
    Min Nonbonded Distance : 1.265
  
  Molprobity Statistics.
    All-atom Clashscore : 6.76
    Ramachandran Plot:
      Outliers :  4.38 %
      Allowed  :  5.11 %
      Favored  : 90.51 %
    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 : 2.29 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -0.31 (0.70), residues: 137
    helix:  0.24 (0.49), residues: 91
    sheet:  None (None), residues: 0
    loop : -0.94 (1.06), residues: 46
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.015   0.004   PHE A  45 
   TYR   0.057   0.010   TYR A 111 
   ARG   0.038   0.010   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.013   0.004   PHE A  67 
   TYR   0.048   0.012   TYR A 111 
   ARG   0.004   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN

=================================== Summary ===================================

  Ramachandran outliers =   4.38 %
                favored =  90.51 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   6.76
  RMS(bonds)            =   0.0089
  RMS(angles)           =   1.58
  MolProbity score      =   2.07

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.024 (Z=  1.491)
  Mean delta:    0.004 (Z=  0.232)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    4.240 (Z=  1.301)
  Mean delta:    0.683 (Z=  0.324)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:   77.761
  Mean delta:   10.507

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.160
  Mean delta:    0.040

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.021
  Mean delta:    0.003

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.003   0.024   2242  Z= 0.166
    Angle     :  1.079   5.122   4079  Z= 0.387
    Chirality :  0.040   0.160    176
    Planarity :  0.002   0.021    327
    Dihedral  : 10.480  77.761    769
    Min Nonbonded Distance : 1.089
  
  Molprobity Statistics.
    All-atom Clashscore : 11.27
    Ramachandran Plot:
      Outliers :  0.73 %
      Allowed  :  0.73 %
      Favored  : 98.54 %
    Rotamer:
      Outliers :  0.81 %
      Allowed  :  0.00 %
      Favored  : 99.19 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  1.13 (0.70), residues: 137
    helix:  0.46 (0.63), residues: 63
    sheet:  None (None), residues: 0
    loop :  1.28 (0.74), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.004   0.001   PHE A  15 
   TYR   0.009   0.002   TYR A  68 
   ARG   0.005   0.001   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 135 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.008   0.002   TYR A 111 
   ARG   0.003   0.001   ARG A  21 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   0.73 %
                favored =  98.54 %
  Rotamer outliers      =   0.81 %
  C-beta deviations     =     0
  Clashscore            =  11.27
  RMS(bonds)            =   0.0027
  RMS(angles)           =   1.08
  MolProbity score      =   1.57

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  1.538)
  Mean delta:    0.004 (Z=  0.241)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001 (Z=  0.000)
  Max. delta:    6.153 (Z=  1.979)
  Mean delta:    0.684 (Z=  0.330)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.007
  Max. delta:   67.606
  Mean delta:    8.237

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.143
  Mean delta:    0.037

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.022
  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   2242  Z= 0.172
    Angle     :  1.059   6.153   4079  Z= 0.382
    Chirality :  0.037   0.143    176
    Planarity :  0.002   0.022    327
    Dihedral  :  8.980  67.606    769
    Min Nonbonded Distance : 1.493
  
  Molprobity Statistics.
    All-atom Clashscore : 13.07
    Ramachandran Plot:
      Outliers :  1.46 %
      Allowed  :  1.46 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 0.00 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole: -1.37 (0.62), residues: 137
    helix: -0.53 (0.56), residues: 70
    sheet:  None (None), residues: 0
    loop : -1.26 (0.65), residues: 67
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 135 
   PHE   0.004   0.001   PHE A  15 
   TYR   0.007   0.002   TYR A  89 
   ARG   0.003   0.001   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.002   HIS A 135 
   PHE   0.002   0.001   PHE A  45 
   TYR   0.005   0.001   TYR A  12 
   ARG   0.002   0.000   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A  66  GLN
   A 136  HIS
   A 137  HIS

=================================== Summary ===================================

  Ramachandran outliers =   1.46 %
                favored =  97.08 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =  13.07
  RMS(bonds)            =   0.0028
  RMS(angles)           =   1.06
  MolProbity score      =   1.79

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.582)
  Mean delta:    0.012 (Z=  0.634)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  28  GLN  OE1
   A  28  GLN  CD
   A  28  GLN  NE2       122.60   118.57     4.03  1.00e+00  1.62e+01   4.0*sigma

  Min. delta:    0.003 (Z=  0.001)
  Max. delta:    6.531 (Z=  4.030)
  Mean delta:    1.609 (Z=  0.882)

                      ----------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   158.54    21.46  5.00e+00  1.84e+01   4.3*sigma

  Min. delta:    0.024
  Max. delta:   85.378
  Mean delta:   12.198

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.246
  Mean delta:    0.079

                       ----------Planar groups----------                       

  atoms                 rms_deltas   delta_max    residual   deviation
   A  81  TYR  CB
   A  81  TYR  CG
   A  81  TYR  CD1
   A  81  TYR  CD2
   A  81  TYR  CE1
   A  81  TYR  CE2
   A  81  TYR  CZ
   A  81  TYR  OH            0.159       0.286      502.92  14.3*sigma

  Min. delta:    0.000
  Max. delta:    0.159
  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      :  0.008   0.040   2242  Z= 0.452
    Angle     :  1.547   6.531   4079  Z= 0.672
    Chirality :  0.079   0.246    176
    Planarity :  0.012   0.149    327
    Dihedral  : 11.418  85.378    769
    Min Nonbonded Distance : 1.668
  
  Molprobity Statistics.
    All-atom Clashscore : 4.96
    Ramachandran Plot:
      Outliers :  2.19 %
      Allowed  :  0.73 %
      Favored  : 97.08 %
    Rotamer:
      Outliers :  3.23 %
      Allowed  :  2.42 %
      Favored  : 94.35 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.49 (0.71), residues: 137
    helix:  0.24 (0.52), residues: 83
    sheet: -1.29 (1.58), residues: 10
    loop :  1.37 (1.08), residues: 44
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.014   0.004   PHE A  45 
   TYR   0.352   0.025   TYR A  81 
   ARG   0.038   0.010   ARG A 127 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.002   0.001   HIS A 139 
   PHE   0.011   0.003   PHE A  67 
   TYR   0.286   0.030   TYR A  81 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================


End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.040 (Z=  2.587)
  Mean delta:    0.012 (Z=  0.629)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    6.838 (Z=  3.988)
  Mean delta:    1.656 (Z=  0.909)

                      ----------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  -153.83   -26.17  5.00e+00  2.74e+01   5.2*sigma
   A  93  LEU  CA
   A  93  LEU  C
   A  94  GLY  N
   A  94  GLY  CA        180.00   158.66    21.34  5.00e+00  1.82e+01   4.3*sigma

  Min. delta:    0.005
  Max. delta:   87.213
  Mean delta:   12.974

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.198
  Mean delta:    0.082

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.066
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.009   0.040   2242  Z= 0.448
    Angle     :  1.576   6.891   4079  Z= 0.688
    Chirality :  0.082   0.198    176
    Planarity :  0.009   0.050    327
    Dihedral  : 11.707  87.213    769
    Min Nonbonded Distance : 1.533
  
  Molprobity Statistics.
    All-atom Clashscore : 3.16
    Ramachandran Plot:
      Outliers :  2.92 %
      Allowed  :  4.38 %
      Favored  : 92.70 %
    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:  0.02 (0.67), residues: 137
    helix:  0.29 (0.49), residues: 88
    sheet:  None (None), residues: 0
    loop : -0.26 (0.94), residues: 49
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.001   HIS A 139 
   PHE   0.016   0.004   PHE A  67 
   TYR   0.081   0.012   TYR A  50 
   ARG   0.054   0.013   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   0.067   0.015   TYR A  50 
   ARG   0.006   0.002   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   2.19 %
                favored =  97.08 %
  Rotamer outliers      =   3.23 %
  C-beta deviations     =     0
  Clashscore            =   4.96
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.55
  MolProbity score      =   1.81

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
  Ramachandran outliers =   2.92 %
                favored =  92.70 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   3.16
  RMS(bonds)            =   0.0085
  RMS(angles)           =   1.58
  MolProbity score      =   1.72

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.001)
  Max. delta:    0.040 (Z=  2.678)
  Mean delta:    0.012 (Z=  0.623)

                        ----------Bond angles----------                        

  atoms                   ideal    model    delta   sigma  residual   deviation
   A  87  GLY  C
   A  88  ASP  N
   A  88  ASP  CA        121.70   130.01    -8.31  1.80e+00  2.13e+01   4.6*sigma

  Min. delta:    0.001 (Z=  0.001)
  Max. delta:    8.619 (Z=  4.617)
  Mean delta:    1.727 (Z=  0.908)

                      ----------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   144.24    35.76  5.00e+00  5.12e+01   7.2*sigma
   A  92  THR  CA
   A  92  THR  C
   A  93  LEU  N
   A  93  LEU  CA        180.00   149.95    30.05  5.00e+00  3.61e+01   6.0*sigma
   A  90  SER  CA
   A  90  SER  C
   A  91  TYR  N
   A  91  TYR  CA        180.00   150.43    29.57  5.00e+00  3.50e+01   5.9*sigma
   A  85  LYS  CA
   A  85  LYS  C
   A  86  ILE  N
   A  86  ILE  CA        180.00   152.33    27.67  5.00e+00  3.06e+01   5.5*sigma
   A  89  TYR  CA
   A  89  TYR  C
   A  90  SER  N
   A  90  SER  CA        180.00   153.90    26.10  5.00e+00  2.73e+01   5.2*sigma
   A  79  LYS  CA
   A  79  LYS  C
   A  80  GLY  N
   A  80  GLY  CA        180.00   156.51    23.49  5.00e+00  2.21e+01   4.7*sigma

  Min. delta:    0.012
  Max. delta:   87.012
  Mean delta:   13.260

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.001
  Max. delta:    0.181
  Mean delta:    0.077

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.044
  Mean delta:    0.012

============================= Hydrogen validation =============================


                ----------H/D atoms in the input model----------               

  Total number of hydrogen atoms : 1106
  Total number of deuterium atoms: 0
  Number of H atoms (protein)    : 1106
  Number of D atoms (protein)    : 0
  Number of H atoms (water)      : 0
  Number of D atoms (water)      : 0
  Number of H atoms (other)      : 0
  Number of D atoms (other)      : 0

                      ----------Water molecules----------                      

  Number of water                            : 0
  Number of water with 0 H (or D)            : 0
  Number of water with 1 H (or D)            : 0
  Number of water with 2 H (or D)            : 0
  Number of water in alternative conformation: 0
  Number of water without oxygen atom        : 0

                    ----------MISSING H or D atoms----------                   

    0" pdbres="HIS A  43  conformer  : HE2, HD1 
    0" pdbres="HIS A 134  conformer  : HE2, HD1 
    0" pdbres="HIS A 135  conformer  : HE2, HD1 
    0" pdbres="HIS A 136  conformer  : HE2, HD1 
    0" pdbres="HIS A 137  conformer  : HE2, HD1 
    0" pdbres="HIS A 138  conformer  : HE2, HD1 
    0" pdbres="HIS A 139  conformer  : HE2, HD1 

============================ Molprobity validation ============================


  Geometry Restraints Library: GeoStd + Monomer Library
  Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
    Bond      :  0.008   0.040   2242  Z= 0.443
    Angle     :  1.613   8.619   4079  Z= 0.690
    Chirality :  0.077   0.181    176
    Planarity :  0.009   0.043    327
    Dihedral  : 11.876  87.012    769
    Min Nonbonded Distance : 1.066
  
  Molprobity Statistics.
    All-atom Clashscore : 5.41
    Ramachandran Plot:
      Outliers :  6.57 %
      Allowed  :  7.30 %
      Favored  : 86.13 %
    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 : 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: -0.61 (0.70), residues: 137
    helix:  0.44 (0.52), residues: 82
    sheet:  None (None), residues: 0
    loop : -1.69 (0.90), residues: 55
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.020   0.004   PHE A  45 
   TYR   0.068   0.010   TYR A  50 
   ARG   0.036   0.011   ARG A  58 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.001   0.000   HIS A 139 
   PHE   0.014   0.005   PHE A  67 
   TYR   0.056   0.012   TYR A  50 
   ARG   0.005   0.001   ARG A 127 

                     ----------Asn/Gln/His flips----------                     

  No backwards Asn/Gln/His sidechains found.

=================================== Summary ===================================

  Ramachandran outliers =   6.57 %
                favored =  86.13 %
  Rotamer outliers      =   1.61 %
  C-beta deviations     =     0
  Clashscore            =   5.41
  RMS(bonds)            =   0.0084
  RMS(angles)           =   1.61
  MolProbity score      =   2.09

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py

End of input processing

=============================== Model properties ==============================

   Number of:
     all atoms      : 2218
     H or D atoms   : 1106
     chains         : 1
     a.a. residues  : 139
     nucleotides    : 0
     water          : 0
     other (ligands): 0
   Ligands: None

============================= Geometry restraints =============================


                        ----------Bond lengths----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    0.022 (Z=  1.543)
  Mean delta:    0.004 (Z=  0.268)

                        ----------Bond angles----------                        

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000 (Z=  0.000)
  Max. delta:    4.053 (Z=  1.615)
  Mean delta:    0.649 (Z=  0.308)

                      ----------Dihedral angles----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:   85.590
  Mean delta:   14.507

                       ----------Chiral volumes----------                      

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.167
  Mean delta:    0.048

                       ----------Planar groups----------                       

  All restrained atoms within 4.0 sigma of ideal values.

  Min. delta:    0.000
  Max. delta:    0.022
  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   2242  Z= 0.191
    Angle     :  1.077   4.860   4079  Z= 0.384
    Chirality :  0.048   0.167    176
    Planarity :  0.002   0.022    327
    Dihedral  : 12.619  85.590    769
    Min Nonbonded Distance : 1.474
  
  Molprobity Statistics.
    All-atom Clashscore : 9.02
    Ramachandran Plot:
      Outliers :  0.00 %
      Allowed  :  4.38 %
      Favored  : 95.62 %
    Rotamer:
      Outliers :  0.00 %
      Allowed  :  0.00 %
      Favored  : 100.00 %
    Cbeta Deviations :  0.00 %
    Peptide Plane:
      Cis-proline     : 14.29 %
      Cis-general     : 0.00 %
      Twisted Proline : 0.00 %
      Twisted General : 0.00 %
  
  Rama-Z (Ramachandran plot Z-score):
  Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
  Scores for whole/helix/sheet/loop are scaled independently;
  therefore, the values are not related in a simple manner.
    whole:  0.40 (0.71), residues: 137
    helix: -0.27 (0.60), residues: 63
    sheet:  None (None), residues: 0
    loop :  1.01 (0.78), residues: 74
  
  Max deviation from planes:
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.006   0.002   PHE A  67 
   TYR   0.018   0.003   TYR A  50 
   ARG   0.005   0.002   ARG A  21 

  Max deviation from planes (no H):
     Type  MaxDev  MeanDev LineInFile
   HIS   0.004   0.001   HIS A 135 
   PHE   0.004   0.002   PHE A  67 
   TYR   0.015   0.004   TYR A  50 
   ARG   0.002   0.001   ARG A  58 

                     ----------Asn/Gln/His flips----------                     

   A 136  HIS

=================================== Summary ===================================

  Ramachandran outliers =   0.00 %
                favored =  95.62 %
  Rotamer outliers      =   0.00 %
  C-beta deviations     =     0
  Clashscore            =   9.02
  RMS(bonds)            =   0.0032
  RMS(angles)           =   1.08
  MolProbity score      =   1.79

Results written to molprobity.out
Wrote script for Coot: molprobity_coot.py
