Starting phenix.real_space_refine
on Sat Aug 23 05:05:57 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8v91_43047/08_2025/8v91_43047.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v91_43047/08_2025/8v91_43047.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v91_43047/08_2025/8v91_43047.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v91_43047/08_2025/8v91_43047.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8v91_43047/08_2025/8v91_43047.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v91_43047/08_2025/8v91_43047.map"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.051
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    6386      2.51       5
     N    1601      2.21       5
     O    1864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9913
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1654
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 9, 'TRANS': 213}
    Chain: "B"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1654
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 9, 'TRANS': 213}
    Chain: "C"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1654
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 9, 'TRANS': 213}
    Chain: "D"
      Number of atoms: 1654
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1654
          Classifications: {'peptide': 223}
          Link IDs: {'PTRANS': 9, 'TRANS': 213}
    Chain: "I"
      Number of atoms: 1626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1626
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 200}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "J"
      Number of atoms: 1584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1584
          Classifications: {'peptide': 216}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 204}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 23
          Classifications: {'water': 23}
          Link IDs: {None: 22}
    Chain: "C"
      Number of atoms: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 22
          Classifications: {'water': 22}
          Link IDs: {None: 21}
    Chain: "D"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 21
          Classifications: {'water': 21}
          Link IDs: {None: 20}
  Time building chain proxies: 2.23, per 1000 atoms: 0.22
  Number of scatterers: 9913
  At special positions: 0
  Unit cell: (85.902, 85.068, 142.614, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    1864      8.00
     N    1601      7.00
     C    6386      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS I  23 " - pdb=" SG  CYS I  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 134 " - pdb=" SG  CYS I 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J 143 " - pdb=" SG  CYS J 199 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 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
  Conformation dependent library (CDL) restraints added in 306.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2360

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      53.8% alpha, 14.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 56
      removed outlier: 3.583A  pdb=" N   THR A  56 " --> pdb=" O   SER A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 93
      removed outlier: 3.597A  pdb=" N   ILE A  73 " --> pdb=" O   ASP A  69 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE A  81 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   HIS A  90 " --> pdb=" O   GLN A  86 " (cutoff:3.500A)
      removed outlier: 5.528A  pdb=" N   ILE A  91 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 107
    Processing helix  chain 'A' and resid 111 through 137
      removed outlier: 3.543A  pdb=" N   PHE A 117 " --> pdb=" O   ALA A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 3.598A  pdb=" N   VAL A 142 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 178
      removed outlier: 3.680A  pdb=" N   LEU A 161 " --> pdb=" O   GLY A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 205
    Processing helix  chain 'A' and resid 213 through 225
      Proline residue:  A 220  - end of helix
    Processing helix  chain 'A' and resid 231 through 251
      Proline residue:  A 237  - end of helix
    Processing helix  chain 'B' and resid 33 through 56
      removed outlier: 3.690A  pdb=" N   THR B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 93
      removed outlier: 3.537A  pdb=" N   ILE B  81 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   HIS B  90 " --> pdb=" O   GLN B  86 " (cutoff:3.500A)
      removed outlier: 5.788A  pdb=" N   ILE B  91 " --> pdb=" O   CYS B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 97 through 107
    Processing helix  chain 'B' and resid 111 through 137
      removed outlier: 3.734A  pdb=" N   PHE B 117 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 142
      removed outlier: 3.572A  pdb=" N   VAL B 142 " --> pdb=" O   PRO B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 178
      removed outlier: 3.562A  pdb=" N   LEU B 161 " --> pdb=" O   GLY B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 188 through 204
    Processing helix  chain 'B' and resid 213 through 225
      Proline residue:  B 220  - end of helix
    Processing helix  chain 'B' and resid 231 through 251
      Proline residue:  B 237  - end of helix
    Processing helix  chain 'C' and resid 33 through 56
      removed outlier: 3.662A  pdb=" N   THR C  56 " --> pdb=" O   SER C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 93
      removed outlier: 3.866A  pdb=" N   ILE C  73 " --> pdb=" O   ASP C  69 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ILE C  81 " --> pdb=" O   PHE C  77 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   HIS C  90 " --> pdb=" O   GLN C  86 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   ILE C  91 " --> pdb=" O   CYS C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 107
    Processing helix  chain 'C' and resid 111 through 137
      removed outlier: 3.780A  pdb=" N   PHE C 117 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 142
      removed outlier: 3.504A  pdb=" N   VAL C 142 " --> pdb=" O   PRO C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 155 through 178
    Processing helix  chain 'C' and resid 188 through 209
      removed outlier: 3.700A  pdb=" N   ILE C 205 " --> pdb=" O   HIS C 201 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   ASN C 206 " --> pdb=" O   LEU C 202 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   TYR C 207 " --> pdb=" O   PHE C 203 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 225
      Proline residue:  C 220  - end of helix
    Processing helix  chain 'C' and resid 231 through 251
      Proline residue:  C 237  - end of helix
    Processing helix  chain 'D' and resid 33 through 56
      removed outlier: 3.714A  pdb=" N   VAL D  49 " --> pdb=" O   MET D  45 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR D  56 " --> pdb=" O   SER D  52 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 69 through 93
      removed outlier: 3.507A  pdb=" N   ILE D  73 " --> pdb=" O   ASP D  69 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ILE D  81 " --> pdb=" O   PHE D  77 " (cutoff:3.500A)
      removed outlier: 5.486A  pdb=" N   HIS D  90 " --> pdb=" O   GLN D  86 " (cutoff:3.500A)
      removed outlier: 5.613A  pdb=" N   ILE D  91 " --> pdb=" O   CYS D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 97 through 107
    Processing helix  chain 'D' and resid 111 through 137
      removed outlier: 3.521A  pdb=" N   PHE D 117 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 138 through 143
      removed outlier: 4.818A  pdb=" N   GLY D 143 " --> pdb=" O   PRO D 139 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 155 through 178
      removed outlier: 3.665A  pdb=" N   LEU D 161 " --> pdb=" O   GLY D 157 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 188 through 205
      removed outlier: 3.709A  pdb=" N   ILE D 205 " --> pdb=" O   HIS D 201 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 225
      Proline residue:  D 220  - end of helix
    Processing helix  chain 'D' and resid 231 through 251
      Proline residue:  D 237  - end of helix
    Processing helix  chain 'I' and resid 79 through 83
      removed outlier: 3.779A  pdb=" N   PHE I  83 " --> pdb=" O   PRO I  80 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 121 through 126
      removed outlier: 3.535A  pdb=" N   LYS I 126 " --> pdb=" O   ASP I 122 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 183 through 188
    Processing helix  chain 'J' and resid 87 through 91
      removed outlier: 3.822A  pdb=" N   THR J  91 " --> pdb=" O   ALA J  88 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 130 through 135
      removed outlier: 3.545A  pdb=" N   SER J 135 " --> pdb=" O   SER J 131 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 188 through 192
    Processing sheet with id=AA1, first strand: chain 'I' and resid 4 through 7
      removed outlier: 3.716A  pdb=" N   ASP I  70 " --> pdb=" O   SER I  67 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'I' and resid 10 through 13
      removed outlier: 6.662A  pdb=" N   LEU I  33 " --> pdb=" O   TYR I  49 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   TYR I  49 " --> pdb=" O   LEU I  33 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   TRP I  35 " --> pdb=" O   LEU I  47 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'I' and resid 114 through 118
      removed outlier: 3.633A  pdb=" N   VAL I 133 " --> pdb=" O   PHE I 118 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   CYS I 134 " --> pdb=" O   SER I 177 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER I 177 " --> pdb=" O   CYS I 134 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   TYR I 173 " --> pdb=" O   ASN I 138 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'I' and resid 153 through 155
      removed outlier: 4.364A  pdb=" N   TRP I 148 " --> pdb=" O   GLN I 155 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   LYS I 145 " --> pdb=" O   THR I 197 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR I 197 " --> pdb=" O   LYS I 145 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   CYS I 194 " --> pdb=" O   LYS I 207 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LYS I 207 " --> pdb=" O   CYS I 194 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'J' and resid 3 through 7
      removed outlier: 3.564A  pdb=" N   GLN J   3 " --> pdb=" O   SER J  25 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'J' and resid 10 through 12
      removed outlier: 6.195A  pdb=" N   GLY J  10 " --> pdb=" O   THR J 113 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   MET J  34 " --> pdb=" O   SER J  50 " (cutoff:3.500A)
      removed outlier: 4.607A  pdb=" N   SER J  50 " --> pdb=" O   MET J  34 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   TRP J  36 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'J' and resid 124 through 127
      removed outlier: 5.432A  pdb=" N   TYR J 179 " --> pdb=" O   ASP J 147 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'J' and resid 124 through 127
      removed outlier: 5.432A  pdb=" N   TYR J 179 " --> pdb=" O   ASP J 147 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'J' and resid 154 through 157
      removed outlier: 3.831A  pdb=" N   CYS J 199 " --> pdb=" O   LYS J 212 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LYS J 212 " --> pdb=" O   CYS J 199 " (cutoff:3.500A)

    608 hydrogen bonds defined for protein.
    1761 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.70

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3046
        1.34 -     1.46: 2547
        1.46 -     1.58: 4388
        1.58 -     1.70: 0
        1.70 -     1.82: 92
  Bond restraints: 10073
  Sorted by residual:
  bond pdb=" CG  ARG J  30 "
       pdb=" CD  ARG J  30 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.37e+00
  bond pdb=" CB  GLU I 161 "
       pdb=" CG  GLU I 161 "
    ideal  model  delta    sigma   weight residual
    1.520  1.554 -0.034 3.00e-02 1.11e+03 1.31e+00
  bond pdb=" CB  GLU I 143 "
       pdb=" CG  GLU I 143 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.21e+00
  bond pdb=" CB  VAL D  49 "
       pdb=" CG1 VAL D  49 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.05e+00
  bond pdb=" CA  GLU I 161 "
       pdb=" CB  GLU I 161 "
    ideal  model  delta    sigma   weight residual
    1.536  1.562 -0.026 2.53e-02 1.56e+03 1.05e+00
  ... (remaining 10068 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 13462
        1.55 -     3.10: 203
        3.10 -     4.66: 46
        4.66 -     6.21: 23
        6.21 -     7.76: 7
  Bond angle restraints: 13741
  Sorted by residual:
  angle pdb=" CA  MET D  45 "
        pdb=" CB  MET D  45 "
        pdb=" CG  MET D  45 "
      ideal   model   delta    sigma   weight residual
     114.10  121.03   -6.93 2.00e+00 2.50e-01 1.20e+01
  angle pdb=" CA  LYS A  64 "
        pdb=" CB  LYS A  64 "
        pdb=" CG  LYS A  64 "
      ideal   model   delta    sigma   weight residual
     114.10  120.18   -6.08 2.00e+00 2.50e-01 9.23e+00
  angle pdb=" CG  ARG J  30 "
        pdb=" CD  ARG J  30 "
        pdb=" NE  ARG J  30 "
      ideal   model   delta    sigma   weight residual
     112.00  118.61   -6.61 2.20e+00 2.07e-01 9.04e+00
  angle pdb=" CA  GLU I 161 "
        pdb=" CB  GLU I 161 "
        pdb=" CG  GLU I 161 "
      ideal   model   delta    sigma   weight residual
     114.10  119.64   -5.54 2.00e+00 2.50e-01 7.66e+00
  angle pdb=" CB  ARG J  30 "
        pdb=" CG  ARG J  30 "
        pdb=" CD  ARG J  30 "
      ideal   model   delta    sigma   weight residual
     111.30  117.59   -6.29 2.30e+00 1.89e-01 7.49e+00
  ... (remaining 13736 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.40: 5207
       16.40 -    32.80: 411
       32.80 -    49.21: 120
       49.21 -    65.61: 35
       65.61 -    82.01: 7
  Dihedral angle restraints: 5780
    sinusoidal: 2062
      harmonic: 3718
  Sorted by residual:
  dihedral pdb=" CB  CYS J 143 "
           pdb=" SG  CYS J 143 "
           pdb=" SG  CYS J 199 "
           pdb=" CB  CYS J 199 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.34  -44.34     1      1.00e+01 1.00e-02 2.73e+01
  dihedral pdb=" CA  PHE C 203 "
           pdb=" C   PHE C 203 "
           pdb=" N   ALA C 204 "
           pdb=" CA  ALA C 204 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.98  -19.02     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  PHE A 203 "
           pdb=" C   PHE A 203 "
           pdb=" N   ALA A 204 "
           pdb=" CA  ALA A 204 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.85  -18.15     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 5777 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1194
       0.042 -    0.084: 321
       0.084 -    0.126: 98
       0.126 -    0.169: 4
       0.169 -    0.211: 1
  Chirality restraints: 1618
  Sorted by residual:
  chirality pdb=" CB  ILE D  96 "
            pdb=" CA  ILE D  96 "
            pdb=" CG1 ILE D  96 "
            pdb=" CG2 ILE D  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  LYS J 204 "
            pdb=" N   LYS J 204 "
            pdb=" C   LYS J 204 "
            pdb=" CB  LYS J 204 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.78e-01
  chirality pdb=" CB  ILE A  96 "
            pdb=" CA  ILE A  96 "
            pdb=" CG1 ILE A  96 "
            pdb=" CG2 ILE A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.78   -0.14 2.00e-01 2.50e+01 4.72e-01
  ... (remaining 1615 not shown)

  Planarity restraints: 1704
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG J  30 "    0.184 9.50e-02 1.11e+02   8.31e-02 5.46e+00
        pdb=" NE  ARG J  30 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG J  30 "    0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG J  30 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG J  30 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL J 187 "    0.038 5.00e-02 4.00e+02   5.79e-02 5.35e+00
        pdb=" N   PRO J 188 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO J 188 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO J 188 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU J 151 "   -0.029 5.00e-02 4.00e+02   4.40e-02 3.09e+00
        pdb=" N   PRO J 152 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO J 152 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO J 152 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1701 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 129
        2.65 -     3.21: 9383
        3.21 -     3.77: 15793
        3.77 -     4.34: 22381
        4.34 -     4.90: 36499
  Nonbonded interactions: 84185
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 163 "
            pdb=" OG1 THR B 208 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" O   GLN D  32 "
            pdb=" NE1 TRP D  35 "
     model   vdw
     2.090 3.120
  nonbonded pdb=" O   ASP J  90 "
            pdb=" OD1 ASP J  90 "
     model   vdw
     2.129 3.040
  nonbonded pdb=" NZ  LYS C 114 "
            pdb=" OH  TYR C 118 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" OG  SER B 140 "
            pdb=" O   HOH B 401 "
     model   vdw
     2.195 3.040
  ... (remaining 84180 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.750
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:8.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10077  Z= 0.108
  Angle     :  0.555   7.761  13749  Z= 0.277
  Chirality :  0.040   0.211   1618
  Planarity :  0.005   0.083   1704
  Dihedral  : 14.092  82.011   3408
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.49 %
    Favored  : 84.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.68 (0.24), residues: 1306
  helix:  0.33 (0.20), residues: 617
  sheet:  1.21 (0.38), residues: 195
  loop :  0.55 (0.31), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG J  30 
 TYR   0.013   0.001   TYR B 118 
 PHE   0.009   0.001   PHE D  48 
 TRP   0.010   0.001   TRP B  59 
 HIS   0.003   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10073)
  covalent geometry    : angle       0.55489 (13741)
  SS BOND              : bond        0.00169 (    4)
  SS BOND              : angle       0.62492 (    8)
  hydrogen bonds       : bond        0.25487 (  597)
  hydrogen bonds       : angle       8.99593 ( 1761)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   64 LYS cc_start: 0.7570 (tptt) cc_final: 0.7269 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.5877
  time to fit residues: 77.3839
Evaluate side-chains
  116 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 129 optimal weight:    4.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
B  86 GLN
C  86 GLN
I  55 GLN
I  89 GLN
** I  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.189622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.160139 restraints weight = 12181.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.4367 rms_B_bonded: 2.45
r_work: 0.4266 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10077  Z= 0.207
  Angle     :  0.637   7.745  13749  Z= 0.333
  Chirality :  0.045   0.151   1618
  Planarity :  0.005   0.049   1704
  Dihedral  :  4.206  22.765   1383
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 12.64 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.23), residues: 1306
  helix:  1.36 (0.20), residues: 628
  sheet:  1.23 (0.36), residues: 202
  loop :  0.40 (0.30), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG J  30 
 TYR   0.014   0.002   TYR B 118 
 PHE   0.015   0.002   PHE A 218 
 TRP   0.012   0.002   TRP D 227 
 HIS   0.005   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (10073)
  covalent geometry    : angle       0.63681 (13741)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       1.20747 (    8)
  hydrogen bonds       : bond        0.05450 (  597)
  hydrogen bonds       : angle       5.59891 ( 1761)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 123
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  108 ARG cc_start: 0.7417 (mtm180) cc_final: 0.7072 (mtm180)
REVERT: B  111 SER cc_start: 0.7337 (OUTLIER) cc_final: 0.7122 (t)
REVERT: B  228 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.8264 (tt0)
REVERT: B  250 TYR cc_start: 0.8584 (m-80) cc_final: 0.8330 (m-80)
REVERT: C   64 LYS cc_start: 0.7244 (tptt) cc_final: 0.6377 (pptt)
REVERT: C  163 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.6475 (mp0)
REVERT: D   50 LEU cc_start: 0.7924 (OUTLIER) cc_final: 0.7685 (tt)
REVERT: I   90 HIS cc_start: 0.6571 (OUTLIER) cc_final: 0.5417 (t70)
REVERT: I  155 GLN cc_start: 0.7678 (tt0) cc_final: 0.6742 (tm-30)
REVERT: J    3 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.7002 (pm20)
REVERT: J   80 TYR cc_start: 0.8056 (m-80) cc_final: 0.7784 (m-80)
REVERT: J  100 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8086 (m-30)
REVERT: J  195 GLN cc_start: 0.7420 (tt0) cc_final: 0.6559 (tp-100)
  outliers start: 39
  outliers final: 12
  residues processed: 145
  average time/residue: 0.6027
  time to fit residues: 93.4027
Evaluate side-chains
  129 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue   62 THR
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  163 GLU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain I residue   21 ILE
Chi-restraints excluded: chain I residue   30 ARG
Chi-restraints excluded: chain I residue   90 HIS
Chi-restraints excluded: chain J residue    3 GLN
Chi-restraints excluded: chain J residue  100 ASP
Chi-restraints excluded: chain J residue  184 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 113 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 89 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
A 201 HIS
B  86 GLN
B  95 HIS
C  86 GLN
I  89 GLN
I 124 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.192607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.162955 restraints weight = 12050.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.4388 rms_B_bonded: 2.45
r_work: 0.4287 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10077  Z= 0.146
  Angle     :  0.561   6.624  13749  Z= 0.289
  Chirality :  0.042   0.138   1618
  Planarity :  0.005   0.045   1704
  Dihedral  :  4.071  21.522   1383
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.97 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.23), residues: 1306
  helix:  1.76 (0.20), residues: 628
  sheet:  1.13 (0.35), residues: 202
  loop :  0.45 (0.31), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J  30 
 TYR   0.013   0.001   TYR D 248 
 PHE   0.012   0.001   PHE A 218 
 TRP   0.010   0.001   TRP C 227 
 HIS   0.003   0.001   HIS B 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (10073)
  covalent geometry    : angle       0.56129 (13741)
  SS BOND              : bond        0.00312 (    4)
  SS BOND              : angle       0.83586 (    8)
  hydrogen bonds       : bond        0.04503 (  597)
  hydrogen bonds       : angle       5.12928 ( 1761)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  108 ARG cc_start: 0.7458 (mtm180) cc_final: 0.7198 (mtm180)
REVERT: B  250 TYR cc_start: 0.8604 (m-80) cc_final: 0.8295 (m-80)
REVERT: C   64 LYS cc_start: 0.7255 (tptt) cc_final: 0.6393 (pptt)
REVERT: I   90 HIS cc_start: 0.6401 (OUTLIER) cc_final: 0.5515 (t70)
REVERT: I  155 GLN cc_start: 0.7598 (tt0) cc_final: 0.6742 (tm-30)
REVERT: J    3 GLN cc_start: 0.7342 (OUTLIER) cc_final: 0.7065 (pm20)
REVERT: J   80 TYR cc_start: 0.7955 (m-80) cc_final: 0.7675 (m-80)
REVERT: J  100 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8065 (m-30)
REVERT: J  195 GLN cc_start: 0.7426 (tt0) cc_final: 0.6553 (tp-100)
  outliers start: 32
  outliers final: 8
  residues processed: 147
  average time/residue: 0.5623
  time to fit residues: 88.2005
Evaluate side-chains
  127 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain I residue   90 HIS
Chi-restraints excluded: chain I residue  136 LEU
Chi-restraints excluded: chain J residue    3 GLN
Chi-restraints excluded: chain J residue  100 ASP
Chi-restraints excluded: chain J residue  184 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 119 optimal weight:    0.0670
   chunk 88 optimal weight:    0.7980
   chunk 105 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 129 optimal weight:    5.9990
   chunk 114 optimal weight:    0.8980
   overall best weight:    0.6718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
B  86 GLN
C  86 GLN
I  89 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4689 r_free = 0.4689 target = 0.192478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.163010 restraints weight = 12127.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.4399 rms_B_bonded: 2.47
r_work: 0.4297 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10077  Z= 0.130
  Angle     :  0.552   7.269  13749  Z= 0.283
  Chirality :  0.041   0.136   1618
  Planarity :  0.005   0.050   1704
  Dihedral  :  3.991  21.755   1383
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.92 %
    Favored  : 81.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.24), residues: 1306
  helix:  1.79 (0.20), residues: 636
  sheet:  1.06 (0.35), residues: 202
  loop :  0.28 (0.31), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG J  30 
 TYR   0.013   0.001   TYR D 248 
 PHE   0.008   0.001   PHE C 218 
 TRP   0.009   0.001   TRP D 227 
 HIS   0.003   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10073)
  covalent geometry    : angle       0.55187 (13741)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       0.83241 (    8)
  hydrogen bonds       : bond        0.04088 (  597)
  hydrogen bonds       : angle       4.94410 ( 1761)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 125
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  108 ARG cc_start: 0.7408 (mtm180) cc_final: 0.7036 (mtm180)
REVERT: B  228 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8216 (tt0)
REVERT: B  250 TYR cc_start: 0.8613 (m-80) cc_final: 0.8311 (m-80)
REVERT: C   64 LYS cc_start: 0.7234 (tptt) cc_final: 0.6419 (pptt)
REVERT: I   24 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7099 (mmm160)
REVERT: I   90 HIS cc_start: 0.6427 (OUTLIER) cc_final: 0.5573 (t70)
REVERT: I  155 GLN cc_start: 0.7582 (tt0) cc_final: 0.6191 (tm-30)
REVERT: J    3 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.7054 (pm20)
REVERT: J   38 ARG cc_start: 0.8871 (ptt180) cc_final: 0.8659 (ptp90)
REVERT: J   80 TYR cc_start: 0.7910 (m-80) cc_final: 0.7603 (m-80)
REVERT: J  100 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.8040 (m-30)
REVERT: J  195 GLN cc_start: 0.7428 (tt0) cc_final: 0.6577 (tp-100)
  outliers start: 35
  outliers final: 13
  residues processed: 147
  average time/residue: 0.5714
  time to fit residues: 89.6523
Evaluate side-chains
  136 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain I residue   21 ILE
Chi-restraints excluded: chain I residue   24 ARG
Chi-restraints excluded: chain I residue   90 HIS
Chi-restraints excluded: chain I residue  136 LEU
Chi-restraints excluded: chain J residue    3 GLN
Chi-restraints excluded: chain J residue  100 ASP
Chi-restraints excluded: chain J residue  184 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 30 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 91 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 102 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
B  86 GLN
C  86 GLN
I  89 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.192556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.162707 restraints weight = 12142.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.4397 rms_B_bonded: 2.47
r_work: 0.4295 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10077  Z= 0.132
  Angle     :  0.549   8.275  13749  Z= 0.281
  Chirality :  0.041   0.137   1618
  Planarity :  0.005   0.059   1704
  Dihedral  :  3.981  21.206   1383
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.59 %
    Favored  : 81.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.24), residues: 1306
  helix:  1.85 (0.20), residues: 636
  sheet:  1.06 (0.35), residues: 202
  loop :  0.27 (0.31), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG J  30 
 TYR   0.013   0.001   TYR D 248 
 PHE   0.008   0.001   PHE A 218 
 TRP   0.008   0.001   TRP D 227 
 HIS   0.003   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10073)
  covalent geometry    : angle       0.54841 (13741)
  SS BOND              : bond        0.00314 (    4)
  SS BOND              : angle       0.82210 (    8)
  hydrogen bonds       : bond        0.04023 (  597)
  hydrogen bonds       : angle       4.86158 ( 1761)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 127
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 MET cc_start: 0.8715 (mmt) cc_final: 0.8468 (mmm)
REVERT: B  108 ARG cc_start: 0.7380 (mtm180) cc_final: 0.7107 (mtm180)
REVERT: B  228 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8197 (tt0)
REVERT: C   64 LYS cc_start: 0.7253 (tptt) cc_final: 0.6438 (pptt)
REVERT: I   24 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.7092 (mmm160)
REVERT: I   50 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8404 (mmmm)
REVERT: I   90 HIS cc_start: 0.6396 (OUTLIER) cc_final: 0.5540 (t70)
REVERT: I  161 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7136 (mp0)
REVERT: J    3 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7044 (pm20)
REVERT: J   80 TYR cc_start: 0.7873 (m-80) cc_final: 0.7606 (m-80)
REVERT: J  100 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8050 (m-30)
REVERT: J  195 GLN cc_start: 0.7427 (tt0) cc_final: 0.6565 (tp-100)
  outliers start: 34
  outliers final: 17
  residues processed: 151
  average time/residue: 0.6219
  time to fit residues: 99.9609
Evaluate side-chains
  140 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 THR
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain B residue   35 TRP
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain I residue   21 ILE
Chi-restraints excluded: chain I residue   24 ARG
Chi-restraints excluded: chain I residue   50 LYS
Chi-restraints excluded: chain I residue   90 HIS
Chi-restraints excluded: chain I residue  136 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue    3 GLN
Chi-restraints excluded: chain J residue  100 ASP
Chi-restraints excluded: chain J residue  184 VAL
Chi-restraints excluded: chain J residue  200 ASN
Chi-restraints excluded: chain J residue  201 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   chunk 111 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   chunk 81 optimal weight:    0.0980
   chunk 66 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
B  86 GLN
C  86 GLN
D 229 ASN
I  89 GLN
I 210 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.193377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.163623 restraints weight = 12169.759|
|-----------------------------------------------------------------------------|
r_work (start): 0.4403 rms_B_bonded: 2.47
r_work: 0.4301 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10077  Z= 0.125
  Angle     :  0.545   8.001  13749  Z= 0.278
  Chirality :  0.041   0.135   1618
  Planarity :  0.005   0.067   1704
  Dihedral  :  3.942  21.719   1383
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 15.78 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.24), residues: 1306
  helix:  1.89 (0.20), residues: 636
  sheet:  1.25 (0.37), residues: 180
  loop :  0.20 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG J  30 
 TYR   0.013   0.001   TYR D 248 
 PHE   0.008   0.001   PHE D 218 
 TRP   0.008   0.001   TRP J  47 
 HIS   0.002   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10073)
  covalent geometry    : angle       0.54435 (13741)
  SS BOND              : bond        0.00308 (    4)
  SS BOND              : angle       0.82203 (    8)
  hydrogen bonds       : bond        0.03882 (  597)
  hydrogen bonds       : angle       4.79096 ( 1761)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 MET cc_start: 0.8715 (mmt) cc_final: 0.8497 (mmm)
REVERT: B  108 ARG cc_start: 0.7378 (mtm180) cc_final: 0.7077 (mtm180)
REVERT: B  228 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8174 (tt0)
REVERT: C   64 LYS cc_start: 0.7254 (tptt) cc_final: 0.6400 (ptmm)
REVERT: I   24 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.7073 (mmm160)
REVERT: I   90 HIS cc_start: 0.6326 (OUTLIER) cc_final: 0.5551 (t70)
REVERT: I  161 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7199 (mp0)
REVERT: J    3 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.7056 (pm20)
REVERT: J   80 TYR cc_start: 0.7901 (m-80) cc_final: 0.7624 (m-80)
REVERT: J  100 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8025 (m-30)
REVERT: J  195 GLN cc_start: 0.7442 (tt0) cc_final: 0.6555 (tp-100)
  outliers start: 35
  outliers final: 11
  residues processed: 146
  average time/residue: 0.5624
  time to fit residues: 87.5988
Evaluate side-chains
  136 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain I residue   20 THR
Chi-restraints excluded: chain I residue   24 ARG
Chi-restraints excluded: chain I residue   90 HIS
Chi-restraints excluded: chain I residue  136 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue    3 GLN
Chi-restraints excluded: chain J residue  100 ASP
Chi-restraints excluded: chain J residue  184 VAL
Chi-restraints excluded: chain J residue  201 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 82 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    0.2980
   chunk 74 optimal weight:    0.8980
   chunk 12 optimal weight:    6.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
B  86 GLN
B 206 ASN
C  86 GLN
C 206 ASN
I  89 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4699 r_free = 0.4699 target = 0.193477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.163764 restraints weight = 12133.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.4407 rms_B_bonded: 2.46
r_work: 0.4305 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.4305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10077  Z= 0.123
  Angle     :  0.540   8.605  13749  Z= 0.277
  Chirality :  0.041   0.134   1618
  Planarity :  0.005   0.071   1704
  Dihedral  :  3.911  21.222   1383
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 16.44 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.24), residues: 1306
  helix:  1.91 (0.20), residues: 636
  sheet:  1.29 (0.37), residues: 180
  loop :  0.19 (0.30), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG J  30 
 TYR   0.013   0.001   TYR D 248 
 PHE   0.008   0.001   PHE A 218 
 TRP   0.008   0.001   TRP J  47 
 HIS   0.002   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10073)
  covalent geometry    : angle       0.53983 (13741)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       0.80467 (    8)
  hydrogen bonds       : bond        0.03813 (  597)
  hydrogen bonds       : angle       4.72524 ( 1761)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   70 MET cc_start: 0.8718 (mmt) cc_final: 0.8476 (mmm)
REVERT: B  108 ARG cc_start: 0.7373 (mtm180) cc_final: 0.7063 (mtm180)
REVERT: B  228 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8152 (tt0)
REVERT: C   64 LYS cc_start: 0.7281 (tptt) cc_final: 0.6424 (ptmm)
REVERT: I   24 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.7077 (mmm160)
REVERT: I   90 HIS cc_start: 0.6297 (OUTLIER) cc_final: 0.5453 (t70)
REVERT: I  161 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7366 (mp0)
REVERT: J    3 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.7049 (pm20)
REVERT: J   80 TYR cc_start: 0.7901 (m-80) cc_final: 0.7627 (m-80)
REVERT: J  100 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8006 (m-30)
REVERT: J  195 GLN cc_start: 0.7389 (tt0) cc_final: 0.6456 (tp-100)
  outliers start: 28
  outliers final: 14
  residues processed: 143
  average time/residue: 0.6095
  time to fit residues: 92.8944
Evaluate side-chains
  138 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain I residue   20 THR
Chi-restraints excluded: chain I residue   21 ILE
Chi-restraints excluded: chain I residue   24 ARG
Chi-restraints excluded: chain I residue   90 HIS
Chi-restraints excluded: chain I residue  136 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue    3 GLN
Chi-restraints excluded: chain J residue  100 ASP
Chi-restraints excluded: chain J residue  184 VAL
Chi-restraints excluded: chain J residue  200 ASN
Chi-restraints excluded: chain J residue  201 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 116 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0370
   chunk 20 optimal weight:    0.5980
   chunk 80 optimal weight:    0.4980
   chunk 96 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 49 optimal weight:    0.6980
   chunk 109 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.4858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
B  86 GLN
B 206 ASN
C  86 GLN
I  89 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.194663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.165199 restraints weight = 12043.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.4421 rms_B_bonded: 2.46
r_work: 0.4321 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10077  Z= 0.114
  Angle     :  0.537   7.770  13749  Z= 0.275
  Chirality :  0.041   0.134   1618
  Planarity :  0.005   0.076   1704
  Dihedral  :  3.875  21.105   1383
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.63 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.24), residues: 1306
  helix:  1.98 (0.20), residues: 632
  sheet:  1.31 (0.37), residues: 180
  loop :  0.19 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG J  30 
 TYR   0.014   0.001   TYR A 233 
 PHE   0.013   0.001   PHE J 125 
 TRP   0.008   0.001   TRP J  47 
 HIS   0.002   0.000   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10073)
  covalent geometry    : angle       0.53677 (13741)
  SS BOND              : bond        0.00298 (    4)
  SS BOND              : angle       0.77415 (    8)
  hydrogen bonds       : bond        0.03644 (  597)
  hydrogen bonds       : angle       4.66831 ( 1761)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  108 ARG cc_start: 0.7349 (mtm180) cc_final: 0.7024 (mtm180)
REVERT: B  228 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8148 (tt0)
REVERT: C   64 LYS cc_start: 0.7307 (tptt) cc_final: 0.6431 (ptmm)
REVERT: I   24 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.7062 (mmm160)
REVERT: I   90 HIS cc_start: 0.6265 (OUTLIER) cc_final: 0.5333 (t70)
REVERT: J   80 TYR cc_start: 0.7869 (m-80) cc_final: 0.7580 (m-80)
REVERT: J  100 ASP cc_start: 0.8498 (OUTLIER) cc_final: 0.8004 (m-30)
REVERT: J  195 GLN cc_start: 0.7434 (tt0) cc_final: 0.6506 (tp-100)
  outliers start: 29
  outliers final: 16
  residues processed: 148
  average time/residue: 0.5160
  time to fit residues: 81.7459
Evaluate side-chains
  140 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 120
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue   96 ILE
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  205 ILE
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain I residue   20 THR
Chi-restraints excluded: chain I residue   21 ILE
Chi-restraints excluded: chain I residue   24 ARG
Chi-restraints excluded: chain I residue   30 ARG
Chi-restraints excluded: chain I residue   90 HIS
Chi-restraints excluded: chain I residue  136 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue  100 ASP
Chi-restraints excluded: chain J residue  184 VAL
Chi-restraints excluded: chain J residue  200 ASN
Chi-restraints excluded: chain J residue  201 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 120 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 105 optimal weight:    7.9990
   chunk 53 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 74 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.8184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
B  86 GLN
C  86 GLN
I  89 GLN
J   3 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.191067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4432 r_free = 0.4432 target = 0.161714 restraints weight = 12067.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.4392 rms_B_bonded: 2.45
r_work: 0.4292 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10077  Z= 0.145
  Angle     :  0.578   8.725  13749  Z= 0.294
  Chirality :  0.042   0.136   1618
  Planarity :  0.005   0.083   1704
  Dihedral  :  4.022  21.397   1383
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 16.92 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.23), residues: 1306
  helix:  1.91 (0.20), residues: 632
  sheet:  1.23 (0.36), residues: 180
  loop :  0.16 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG J  30 
 TYR   0.018   0.001   TYR A 233 
 PHE   0.008   0.001   PHE A 218 
 TRP   0.009   0.001   TRP B  59 
 HIS   0.003   0.001   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10073)
  covalent geometry    : angle       0.57795 (13741)
  SS BOND              : bond        0.00309 (    4)
  SS BOND              : angle       0.88552 (    8)
  hydrogen bonds       : bond        0.04060 (  597)
  hydrogen bonds       : angle       4.74890 ( 1761)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: B  108 ARG cc_start: 0.7332 (mtm180) cc_final: 0.6997 (mtm180)
REVERT: B  206 ASN cc_start: 0.8596 (m110) cc_final: 0.8250 (m-40)
REVERT: B  228 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8154 (tt0)
REVERT: C   64 LYS cc_start: 0.7306 (tptt) cc_final: 0.6423 (ptmm)
REVERT: I   24 ARG cc_start: 0.7289 (OUTLIER) cc_final: 0.7081 (mmm160)
REVERT: I   90 HIS cc_start: 0.6386 (OUTLIER) cc_final: 0.5503 (t70)
REVERT: J   80 TYR cc_start: 0.7894 (m-80) cc_final: 0.7612 (m-80)
REVERT: J  100 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8059 (m-30)
REVERT: J  195 GLN cc_start: 0.7475 (tt0) cc_final: 0.6533 (tp-100)
  outliers start: 29
  outliers final: 14
  residues processed: 141
  average time/residue: 0.5257
  time to fit residues: 79.2513
Evaluate side-chains
  132 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain D residue  228 GLU
Chi-restraints excluded: chain I residue   20 THR
Chi-restraints excluded: chain I residue   21 ILE
Chi-restraints excluded: chain I residue   24 ARG
Chi-restraints excluded: chain I residue   30 ARG
Chi-restraints excluded: chain I residue   90 HIS
Chi-restraints excluded: chain I residue  136 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue  100 ASP
Chi-restraints excluded: chain J residue  144 LEU
Chi-restraints excluded: chain J residue  184 VAL
Chi-restraints excluded: chain J residue  200 ASN
Chi-restraints excluded: chain J residue  201 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 47 optimal weight:    0.0270
   chunk 54 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0770
   chunk 101 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.3996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
B  86 GLN
C  86 GLN
I  89 GLN
J   3 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.194298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.165133 restraints weight = 11947.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.4427 rms_B_bonded: 2.46
r_work: 0.4329 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.4329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10077  Z= 0.114
  Angle     :  0.551   8.692  13749  Z= 0.281
  Chirality :  0.041   0.133   1618
  Planarity :  0.005   0.082   1704
  Dihedral  :  3.911  20.456   1383
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 17.78 %
    Favored  : 80.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.24), residues: 1306
  helix:  1.97 (0.20), residues: 632
  sheet:  1.26 (0.37), residues: 180
  loop :  0.17 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG J  30 
 TYR   0.017   0.001   TYR A 233 
 PHE   0.018   0.001   PHE J 125 
 TRP   0.007   0.001   TRP I  32 
 HIS   0.002   0.000   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10073)
  covalent geometry    : angle       0.55052 (13741)
  SS BOND              : bond        0.00304 (    4)
  SS BOND              : angle       0.77728 (    8)
  hydrogen bonds       : bond        0.03621 (  597)
  hydrogen bonds       : angle       4.68012 ( 1761)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2612 Ramachandran restraints generated.
    1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
REVERT: B  108 ARG cc_start: 0.7317 (mtm180) cc_final: 0.6981 (mtm180)
REVERT: B  206 ASN cc_start: 0.8583 (m110) cc_final: 0.8316 (m-40)
REVERT: B  228 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8160 (tt0)
REVERT: C   64 LYS cc_start: 0.7316 (tptt) cc_final: 0.6453 (ptmm)
REVERT: D  108 ARG cc_start: 0.7264 (mtp85) cc_final: 0.6867 (mmt90)
REVERT: I   24 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.7052 (mmm160)
REVERT: I   90 HIS cc_start: 0.6181 (OUTLIER) cc_final: 0.5353 (t70)
REVERT: J   80 TYR cc_start: 0.7859 (m-80) cc_final: 0.7576 (m-80)
REVERT: J  100 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8002 (m-30)
REVERT: J  195 GLN cc_start: 0.7470 (tt0) cc_final: 0.6523 (tp-100)
  outliers start: 21
  outliers final: 14
  residues processed: 138
  average time/residue: 0.4913
  time to fit residues: 72.5359
Evaluate side-chains
  136 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain B residue   63 GLU
Chi-restraints excluded: chain B residue  114 LYS
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  228 GLU
Chi-restraints excluded: chain C residue   62 THR
Chi-restraints excluded: chain D residue   62 THR
Chi-restraints excluded: chain I residue   20 THR
Chi-restraints excluded: chain I residue   21 ILE
Chi-restraints excluded: chain I residue   24 ARG
Chi-restraints excluded: chain I residue   30 ARG
Chi-restraints excluded: chain I residue   90 HIS
Chi-restraints excluded: chain I residue  136 LEU
Chi-restraints excluded: chain I residue  196 VAL
Chi-restraints excluded: chain J residue  100 ASP
Chi-restraints excluded: chain J residue  144 LEU
Chi-restraints excluded: chain J residue  184 VAL
Chi-restraints excluded: chain J residue  201 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 124 optimal weight:    3.9990
   chunk 110 optimal weight:    0.5980
   chunk 104 optimal weight:    0.0980
   chunk 2 optimal weight:    0.0980
   chunk 35 optimal weight:    0.9990
   chunk 119 optimal weight:    0.7980
   chunk 127 optimal weight:    0.9980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
A 153 ASN
B  86 GLN
B 153 ASN
B 206 ASN
C  86 GLN
I  89 GLN
J   3 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.194188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.164977 restraints weight = 12089.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.4428 rms_B_bonded: 2.46
r_work: 0.4331 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.4331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10077  Z= 0.118
  Angle     :  0.564   8.567  13749  Z= 0.288
  Chirality :  0.041   0.133   1618
  Planarity :  0.005   0.084   1704
  Dihedral  :  3.926  20.780   1383
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 17.78 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.62 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.76 (0.24), residues: 1306
  helix:  1.97 (0.20), residues: 632
  sheet:  1.27 (0.37), residues: 180
  loop :  0.15 (0.30), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG J  30 
 TYR   0.017   0.001   TYR A 233 
 PHE   0.022   0.001   PHE J 125 
 TRP   0.009   0.001   TRP D 227 
 HIS   0.003   0.000   HIS B 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10073)
  covalent geometry    : angle       0.56377 (13741)
  SS BOND              : bond        0.00313 (    4)
  SS BOND              : angle       0.81057 (    8)
  hydrogen bonds       : bond        0.03655 (  597)
  hydrogen bonds       : angle       4.66182 ( 1761)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3108.96 seconds
wall clock time: 53 minutes 50.67 seconds (3230.67 seconds total)