Starting phenix.real_space_refine
on Fri Feb 14 07:26:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g16_29663/02_2025/8g16_29663.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g16_29663/02_2025/8g16_29663.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g16_29663/02_2025/8g16_29663.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g16_29663/02_2025/8g16_29663.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g16_29663/02_2025/8g16_29663.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g16_29663/02_2025/8g16_29663.cif"
  }
  resolution = 2.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.000 sd=   0.001
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: 5
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6388      2.51       5
     N    1756      2.21       5
     O    1912      1.98       5
     H       4      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10108
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2527
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2527
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 2527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2527
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 2527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2527
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 321}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.84, per 1000 atoms: 0.58
  Number of scatterers: 10108
  At special positions: 0
  Unit cell: (99.365, 102.705, 91.015, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      48     16.00
     O    1912      8.00
     N    1756      7.00
     C    6388      6.00
     H       4      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.50
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2408

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 9 sheets defined
      36.8% alpha, 24.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 26
    Processing helix  chain 'A' and resid 39 through 49
    Processing helix  chain 'A' and resid 81 through 85
      removed outlier: 3.548A  pdb=" N   ILE A  85 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 109
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 136 through 140
      removed outlier: 3.553A  pdb=" N   TYR A 140 " --> pdb=" O   HIS A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 169
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 196 through 200
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 4.038A  pdb=" N   GLY A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 225
    Processing helix  chain 'A' and resid 254 through 268
    Processing helix  chain 'A' and resid 282 through 287
      removed outlier: 3.504A  pdb=" N   ASN A 287 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 334
    Processing helix  chain 'B' and resid 12 through 26
    Processing helix  chain 'B' and resid 39 through 49
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.562A  pdb=" N   ILE B  85 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 109
    Processing helix  chain 'B' and resid 110 through 113
    Processing helix  chain 'B' and resid 136 through 140
      removed outlier: 3.553A  pdb=" N   TYR B 140 " --> pdb=" O   HIS B 137 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 169
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 196 through 200
    Processing helix  chain 'B' and resid 212 through 221
      removed outlier: 4.022A  pdb=" N   GLY B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LYS B 219 " --> pdb=" O   LYS B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 225
    Processing helix  chain 'B' and resid 254 through 268
    Processing helix  chain 'B' and resid 282 through 287
      removed outlier: 3.504A  pdb=" N   ASN B 287 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 334
    Processing helix  chain 'C' and resid 12 through 26
    Processing helix  chain 'C' and resid 39 through 49
    Processing helix  chain 'C' and resid 81 through 85
      removed outlier: 3.549A  pdb=" N   ILE C  85 " --> pdb=" O   PRO C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 104 through 109
    Processing helix  chain 'C' and resid 110 through 113
    Processing helix  chain 'C' and resid 136 through 140
      removed outlier: 3.553A  pdb=" N   TYR C 140 " --> pdb=" O   HIS C 137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 169
      Proline residue:  C 159  - end of helix
    Processing helix  chain 'C' and resid 196 through 200
    Processing helix  chain 'C' and resid 212 through 221
      removed outlier: 3.924A  pdb=" N   GLY C 218 " --> pdb=" O   ALA C 214 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LYS C 219 " --> pdb=" O   LYS C 215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 225
    Processing helix  chain 'C' and resid 254 through 268
    Processing helix  chain 'C' and resid 282 through 287
      removed outlier: 3.504A  pdb=" N   ASN C 287 " --> pdb=" O   SER C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 317 through 334
    Processing helix  chain 'D' and resid 12 through 26
    Processing helix  chain 'D' and resid 39 through 49
    Processing helix  chain 'D' and resid 81 through 85
      removed outlier: 3.562A  pdb=" N   ILE D  85 " --> pdb=" O   PRO D  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 109
    Processing helix  chain 'D' and resid 110 through 113
    Processing helix  chain 'D' and resid 136 through 140
      removed outlier: 3.553A  pdb=" N   TYR D 140 " --> pdb=" O   HIS D 137 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 151 through 169
      Proline residue:  D 159  - end of helix
    Processing helix  chain 'D' and resid 196 through 200
    Processing helix  chain 'D' and resid 212 through 221
      removed outlier: 4.033A  pdb=" N   GLY D 218 " --> pdb=" O   ALA D 214 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS D 219 " --> pdb=" O   LYS D 215 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 222 through 225
    Processing helix  chain 'D' and resid 254 through 268
    Processing helix  chain 'D' and resid 282 through 287
      removed outlier: 3.504A  pdb=" N   ASN D 287 " --> pdb=" O   SER D 284 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 317 through 334
    Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63
      removed outlier: 10.263A  pdb=" N   ASP A  29 " --> pdb=" O   PRO A  73 " (cutoff:3.500A)
      removed outlier: 9.947A  pdb=" N   THR A  75 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   VAL A  31 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
      removed outlier: 8.127A  pdb=" N   PHE A  77 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   ILE A  33 " --> pdb=" O   PHE A  77 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   VAL A   8 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ILE A  33 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   VAL A  95 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210
      removed outlier: 3.629A  pdb=" N   THR A 229 " --> pdb=" O   GLY A 173 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU A 172 " --> pdb=" O   ARG A 248 " (cutoff:3.500A)
      removed outlier: 12.311A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
      removed outlier: 11.141A  pdb=" N   GLY A 300 " --> pdb=" O   PHE A 307 " (cutoff:3.500A)
      removed outlier: 10.874A  pdb=" N   LYS A 309 " --> pdb=" O   GLY A 298 " (cutoff:3.500A)
      removed outlier: 8.936A  pdb=" N   GLY A 298 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
      removed outlier: 4.741A  pdb=" N   ILE A 311 " --> pdb=" O   ASP A 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63
      removed outlier: 10.262A  pdb=" N   ASP B  29 " --> pdb=" O   PRO B  73 " (cutoff:3.500A)
      removed outlier: 9.940A  pdb=" N   THR B  75 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL B  31 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   PHE B  77 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   ILE B  33 " --> pdb=" O   PHE B  77 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   VAL B   8 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ILE B  33 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL B  95 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.701A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU B 172 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 4.783A  pdb=" N   ILE B 311 " --> pdb=" O   ASP B 296 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 208 through 210
      removed outlier: 3.701A  pdb=" N   THR B 229 " --> pdb=" O   GLY B 173 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU B 172 " --> pdb=" O   ARG B 248 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   PHE B 307 " --> pdb=" O   LEU B 303 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 63
      removed outlier: 10.262A  pdb=" N   ASP C  29 " --> pdb=" O   PRO C  73 " (cutoff:3.500A)
      removed outlier: 9.943A  pdb=" N   THR C  75 " --> pdb=" O   ASP C  29 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   VAL C  31 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 8.126A  pdb=" N   PHE C  77 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   ILE C  33 " --> pdb=" O   PHE C  77 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   VAL C   8 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ILE C  33 " --> pdb=" O   VAL C   8 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   VAL C  95 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 208 through 210
      removed outlier: 3.673A  pdb=" N   THR C 229 " --> pdb=" O   GLY C 173 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU C 172 " --> pdb=" O   ARG C 248 " (cutoff:3.500A)
      removed outlier: 12.307A  pdb=" N   PHE C 307 " --> pdb=" O   GLY C 300 " (cutoff:3.500A)
      removed outlier: 11.136A  pdb=" N   GLY C 300 " --> pdb=" O   PHE C 307 " (cutoff:3.500A)
      removed outlier: 10.890A  pdb=" N   LYS C 309 " --> pdb=" O   GLY C 298 " (cutoff:3.500A)
      removed outlier: 8.939A  pdb=" N   GLY C 298 " --> pdb=" O   LYS C 309 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   ILE C 311 " --> pdb=" O   ASP C 296 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 63
      removed outlier: 10.261A  pdb=" N   ASP D  29 " --> pdb=" O   PRO D  73 " (cutoff:3.500A)
      removed outlier: 9.943A  pdb=" N   THR D  75 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL D  31 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 8.135A  pdb=" N   PHE D  77 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   ILE D  33 " --> pdb=" O   PHE D  77 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   VAL D   8 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ILE D  33 " --> pdb=" O   VAL D   8 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   VAL D  95 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.683A  pdb=" N   THR D 229 " --> pdb=" O   GLY D 173 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   GLU D 172 " --> pdb=" O   ARG D 248 " (cutoff:3.500A)
      removed outlier: 12.309A  pdb=" N   PHE D 307 " --> pdb=" O   GLY D 300 " (cutoff:3.500A)
      removed outlier: 11.140A  pdb=" N   GLY D 300 " --> pdb=" O   PHE D 307 " (cutoff:3.500A)
      removed outlier: 10.873A  pdb=" N   LYS D 309 " --> pdb=" O   GLY D 298 " (cutoff:3.500A)
      removed outlier: 8.937A  pdb=" N   GLY D 298 " --> pdb=" O   LYS D 309 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   ILE D 311 " --> pdb=" O   ASP D 296 " (cutoff:3.500A)

    480 hydrogen bonds defined for protein.
    1305 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: 3.41

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        0.97 -     1.14: 4
        1.14 -     1.31: 1709
        1.31 -     1.47: 3988
        1.47 -     1.64: 4523
        1.64 -     1.81: 84
  Bond restraints: 10308
  Sorted by residual:
  bond pdb=" N   VAL D 188 "
       pdb=" CA  VAL D 188 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.23e-02 6.61e+03 9.97e+00
  bond pdb=" N   ASN D 142 "
       pdb=" CA  ASN D 142 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.61e+00
  bond pdb=" N   ASN C 142 "
       pdb=" CA  ASN C 142 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.61e+00
  bond pdb=" N   ASN B 142 "
       pdb=" CA  ASN B 142 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.61e+00
  bond pdb=" N   ASN A 142 "
       pdb=" CA  ASN A 142 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.29e-02 6.01e+03 9.61e+00
  ... (remaining 10303 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 13843
        2.96 -     5.92: 96
        5.92 -     8.88: 9
        8.88 -    11.85: 0
       11.85 -    14.81: 8
  Bond angle restraints: 13956
  Sorted by residual:
  angle pdb=" N   ILE B 207 "
        pdb=" CA  ILE B 207 "
        pdb=" C   ILE B 207 "
      ideal   model   delta    sigma   weight residual
     108.88  122.74  -13.86 2.16e+00 2.14e-01 4.12e+01
  angle pdb=" N   ILE D 207 "
        pdb=" CA  ILE D 207 "
        pdb=" C   ILE D 207 "
      ideal   model   delta    sigma   weight residual
     108.88  122.70  -13.82 2.16e+00 2.14e-01 4.09e+01
  angle pdb=" N   ILE A 207 "
        pdb=" CA  ILE A 207 "
        pdb=" C   ILE A 207 "
      ideal   model   delta    sigma   weight residual
     108.88  122.70  -13.82 2.16e+00 2.14e-01 4.09e+01
  angle pdb=" N   ILE C 207 "
        pdb=" CA  ILE C 207 "
        pdb=" C   ILE C 207 "
      ideal   model   delta    sigma   weight residual
     108.88  122.69  -13.81 2.16e+00 2.14e-01 4.09e+01
  angle pdb=" CA  LEU C 203 "
        pdb=" CB  LEU C 203 "
        pdb=" CG  LEU C 203 "
      ideal   model   delta    sigma   weight residual
     116.30  131.11  -14.81 3.50e+00 8.16e-02 1.79e+01
  ... (remaining 13951 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 5387
       17.31 -    34.61: 512
       34.61 -    51.92: 160
       51.92 -    69.23: 52
       69.23 -    86.53: 11
  Dihedral angle restraints: 6122
    sinusoidal: 2346
      harmonic: 3776
  Sorted by residual:
  dihedral pdb=" CA  GLN A 204 "
           pdb=" C   GLN A 204 "
           pdb=" N   ASN A 205 "
           pdb=" CA  ASN A 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.98  -18.02     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  GLN D 204 "
           pdb=" C   GLN D 204 "
           pdb=" N   ASN D 205 "
           pdb=" CA  ASN D 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.02  -17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  GLN C 204 "
           pdb=" C   GLN C 204 "
           pdb=" N   ASN C 205 "
           pdb=" CA  ASN C 205 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.04  -17.96     0      5.00e+00 4.00e-02 1.29e+01
  ... (remaining 6119 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1226
       0.058 -    0.115: 285
       0.115 -    0.173: 57
       0.173 -    0.231: 4
       0.231 -    0.288: 4
  Chirality restraints: 1576
  Sorted by residual:
  chirality pdb=" CA  ILE B 207 "
            pdb=" N   ILE B 207 "
            pdb=" C   ILE B 207 "
            pdb=" CB  ILE B 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.15    0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" CA  ILE A 207 "
            pdb=" N   ILE A 207 "
            pdb=" C   ILE A 207 "
            pdb=" CB  ILE A 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.15    0.29 2.00e-01 2.50e+01 2.07e+00
  chirality pdb=" CA  ILE D 207 "
            pdb=" N   ILE D 207 "
            pdb=" C   ILE D 207 "
            pdb=" CB  ILE D 207 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.15    0.29 2.00e-01 2.50e+01 2.04e+00
  ... (remaining 1573 not shown)

  Planarity restraints: 1804
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 318 "    0.019 2.00e-02 2.50e+03   3.91e-02 1.53e+01
        pdb=" C   PHE C 318 "   -0.068 2.00e-02 2.50e+03
        pdb=" O   PHE C 318 "    0.025 2.00e-02 2.50e+03
        pdb=" N   GLY C 319 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 318 "   -0.019 2.00e-02 2.50e+03   3.91e-02 1.53e+01
        pdb=" C   PHE A 318 "    0.068 2.00e-02 2.50e+03
        pdb=" O   PHE A 318 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   GLY A 319 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 318 "   -0.019 2.00e-02 2.50e+03   3.91e-02 1.53e+01
        pdb=" C   PHE B 318 "    0.068 2.00e-02 2.50e+03
        pdb=" O   PHE B 318 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   GLY B 319 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1801 not shown)

  Histogram of nonbonded interaction distances:
        0.80 -     1.56: 15
        1.56 -     2.32: 33
        2.32 -     3.08: 6414
        3.08 -     3.84: 21234
        3.84 -     4.60: 33902
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions: 61598
  Sorted by model distance:
  nonbonded pdb=" ND1 HIS A 179 "
            pdb=" NH1 ARG A 234 "
     model   vdw
     0.795 3.100
  nonbonded pdb=" ND1 HIS C 179 "
            pdb=" NH1 ARG C 234 "
     model   vdw
     0.802 3.100
  nonbonded pdb=" ND1 HIS D 179 "
            pdb=" NH1 ARG D 234 "
     model   vdw
     0.808 3.100
  nonbonded pdb=" ND1 HIS B 179 "
            pdb=" NH1 ARG B 234 "
     model   vdw
     0.809 3.100
  nonbonded pdb=" CG  HIS B 179 "
            pdb=" NH1 ARG B 234 "
     model   vdw
     0.959 3.300
  ... (remaining 61593 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: 0.04
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:             0.860
  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:             0.220
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.030
  Find NCS groups from input model:        0.340
  Set up NCS constraints:                  0.040
  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:             0.000
  Load rotamer database and sin/cos tables:11.450
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8906
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      :  0.004   0.041  10304  Z= 0.279
  Angle     :  0.793  14.807  13944  Z= 0.459
  Chirality :  0.053   0.288   1576
  Planarity :  0.007   0.081   1804
  Dihedral  : 16.155  86.532   3714
  Min Nonbonded Distance : 0.795

Molprobity Statistics.
  All-atom Clashscore : 4.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.72 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.22), residues: 1328
  helix: -0.98 (0.23), residues: 348
  sheet: -0.14 (0.38), residues: 220
  loop : -0.91 (0.22), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  87 
 HIS   0.002   0.001   HIS B  53 
 PHE   0.006   0.001   PHE B  11 
 TYR   0.008   0.001   TYR C 314 
 ARG   0.002   0.000   ARG C 323 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 13
  outliers final: 9
  residues processed: 104
  average time/residue: 1.5157
  time to fit residues: 168.2090
Evaluate side-chains
  85 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue  220 VAL
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue  220 VAL
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:   20.0000
   chunk 100 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 40 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 119 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 185 GLN
B 185 GLN
C 185 GLN
D 185 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.089273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.074716 restraints weight = 16811.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3176 rms_B_bonded: 2.06
r_work: 0.3051 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8999
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070  10304  Z= 0.357
  Angle     :  0.599   8.872  13944  Z= 0.332
  Chirality :  0.048   0.146   1576
  Planarity :  0.006   0.068   1804
  Dihedral  :  5.327  32.312   1422
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.01 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.05 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.23), residues: 1328
  helix:  0.70 (0.26), residues: 364
  sheet:  0.08 (0.37), residues: 204
  loop : -0.46 (0.24), residues: 760

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  87 
 HIS   0.007   0.001   HIS C 179 
 PHE   0.014   0.002   PHE A 318 
 TYR   0.015   0.002   TYR D 314 
 ARG   0.008   0.001   ARG A  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 1.109 
Fit side-chains
REVERT: A  142 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8403 (t0)
REVERT: B  142 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8400 (t0)
REVERT: C  142 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8398 (t0)
REVERT: D  142 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8388 (t0)
  outliers start: 25
  outliers final: 8
  residues processed: 91
  average time/residue: 1.6179
  time to fit residues: 156.1958
Evaluate side-chains
  76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  142 ASN
Chi-restraints excluded: chain D residue  203 LEU
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 78 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   chunk 121 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 108 optimal weight:    8.9990
   chunk 101 optimal weight:    6.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    4.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.087634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.073300 restraints weight = 17280.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.3146 rms_B_bonded: 2.06
r_work: 0.3028 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9006
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.092  10304  Z= 0.466
  Angle     :  0.700  14.862  13944  Z= 0.380
  Chirality :  0.051   0.164   1576
  Planarity :  0.009   0.207   1804
  Dihedral  :  5.382  34.554   1416
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.12 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.24), residues: 1328
  helix:  0.90 (0.26), residues: 364
  sheet: -0.02 (0.36), residues: 216
  loop : -0.38 (0.24), residues: 748

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  87 
 HIS   0.003   0.001   HIS C  53 
 PHE   0.011   0.002   PHE D 286 
 TYR   0.015   0.002   TYR B 314 
 ARG   0.009   0.001   ARG B 234 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 67
  time to evaluate  : 1.208 
Fit side-chains
REVERT: A  142 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8453 (t0)
REVERT: B  142 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8449 (t0)
REVERT: C  142 ASN cc_start: 0.8775 (OUTLIER) cc_final: 0.8457 (t0)
REVERT: D  142 ASN cc_start: 0.8763 (OUTLIER) cc_final: 0.8446 (t0)
  outliers start: 38
  outliers final: 17
  residues processed: 90
  average time/residue: 1.6953
  time to fit residues: 162.1020
Evaluate side-chains
  90 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue   64 ASN
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue   64 ASN
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue   64 ASN
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  142 ASN
Chi-restraints excluded: chain D residue  203 LEU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0980
   chunk 93 optimal weight:    0.9980
   chunk 117 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 120 optimal weight:   10.0000
   chunk 31 optimal weight:    4.9990
   chunk 12 optimal weight:   20.0000
   chunk 87 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   overall best weight:    3.0186

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

Flipped N/Q/H residues before XYZ refinement:
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.088895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.074814 restraints weight = 17160.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.06
r_work: 0.3062 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2950 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8987
moved from start:          0.1514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  10304  Z= 0.306
  Angle     :  0.678  16.124  13944  Z= 0.357
  Chirality :  0.047   0.245   1576
  Planarity :  0.009   0.170   1804
  Dihedral  :  6.820 167.264   1416
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.58 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.24), residues: 1328
  helix:  1.21 (0.26), residues: 368
  sheet: -0.07 (0.33), residues: 272
  loop : -0.05 (0.26), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 313 
 HIS   0.002   0.001   HIS C  53 
 PHE   0.010   0.001   PHE C 233 
 TYR   0.011   0.001   TYR B 314 
 ARG   0.019   0.002   ARG A 234 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 70
  time to evaluate  : 1.199 
Fit side-chains
REVERT: A  142 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8477 (t0)
REVERT: B  142 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8472 (t0)
REVERT: C  142 ASN cc_start: 0.8767 (OUTLIER) cc_final: 0.8476 (t0)
REVERT: D  142 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8466 (t0)
  outliers start: 34
  outliers final: 21
  residues processed: 94
  average time/residue: 1.7003
  time to fit residues: 169.4915
Evaluate side-chains
  87 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 62
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  203 LEU
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  266 SER
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  142 ASN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  266 SER
Chi-restraints excluded: chain D residue  318 PHE
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 97 optimal weight:    8.9990
   chunk 96 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 17 optimal weight:    6.9990
   chunk 59 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 93 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
B 264 GLN
C 264 GLN
D 264 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.090531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.076500 restraints weight = 17154.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.08
r_work: 0.3093 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8960
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10304  Z= 0.231
  Angle     :  0.606  15.841  13944  Z= 0.327
  Chirality :  0.046   0.244   1576
  Planarity :  0.007   0.113   1804
  Dihedral  :  9.149 167.893   1416
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.40 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.24), residues: 1328
  helix:  1.42 (0.26), residues: 372
  sheet:  0.02 (0.34), residues: 268
  loop : -0.02 (0.26), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.003   0.000   HIS B 179 
 PHE   0.009   0.001   PHE D 233 
 TYR   0.009   0.001   TYR B 314 
 ARG   0.011   0.001   ARG A  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 69
  time to evaluate  : 1.173 
Fit side-chains
REVERT: A  142 ASN cc_start: 0.8652 (OUTLIER) cc_final: 0.8436 (t0)
REVERT: B  142 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8425 (t0)
REVERT: C  142 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8427 (t0)
REVERT: D  142 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8421 (t0)
  outliers start: 37
  outliers final: 16
  residues processed: 93
  average time/residue: 1.5292
  time to fit residues: 151.8141
Evaluate side-chains
  84 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 64
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  142 ASN
Chi-restraints excluded: chain A residue  243 VAL
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  142 ASN
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  266 SER
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  142 ASN
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  142 ASN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  266 SER
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 70 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9990
   chunk 62 optimal weight:   10.0000
   chunk 54 optimal weight:    0.0470
   overall best weight:    0.7880

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

Flipped N/Q/H residues before XYZ refinement:
B 264 GLN
C 264 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.093117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.079734 restraints weight = 17156.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 2.05
r_work: 0.3167 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8899
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10304  Z= 0.125
  Angle     :  0.517  10.097  13944  Z= 0.276
  Chirality :  0.044   0.182   1576
  Planarity :  0.005   0.077   1804
  Dihedral  :  4.503  24.742   1416
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.51 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.25), residues: 1328
  helix:  2.06 (0.27), residues: 372
  sheet: -0.08 (0.34), residues: 268
  loop :  0.22 (0.27), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.003   0.000   HIS A 179 
 PHE   0.007   0.001   PHE B 233 
 TYR   0.006   0.001   TYR B 276 
 ARG   0.012   0.001   ARG D  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 1.111 
Fit side-chains
  outliers start: 24
  outliers final: 9
  residues processed: 94
  average time/residue: 1.5389
  time to fit residues: 154.0341
Evaluate side-chains
  75 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  266 SER
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  266 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 122 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 50 optimal weight:    9.9990
   chunk 72 optimal weight:    5.9990
   chunk 58 optimal weight:    0.3980
   chunk 109 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 112 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
B 330 HIS
C 264 GLN
C 330 HIS
D 330 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.090599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.076529 restraints weight = 17323.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 2.10
r_work: 0.3095 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8955
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  10304  Z= 0.228
  Angle     :  0.668  23.745  13944  Z= 0.350
  Chirality :  0.048   0.325   1576
  Planarity :  0.009   0.151   1804
  Dihedral  :  6.429 163.246   1412
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.33 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.78 (0.25), residues: 1328
  helix:  1.88 (0.26), residues: 372
  sheet: -0.13 (0.33), residues: 272
  loop :  0.13 (0.27), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.002   0.001   HIS C 179 
 PHE   0.008   0.001   PHE B 233 
 TYR   0.010   0.001   TYR B 314 
 ARG   0.013   0.001   ARG C  80 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 1.190 
Fit side-chains
  outliers start: 26
  outliers final: 12
  residues processed: 83
  average time/residue: 1.4879
  time to fit residues: 132.1143
Evaluate side-chains
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  318 PHE
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0670
   chunk 18 optimal weight:    6.9990
   chunk 5 optimal weight:    0.0060
   chunk 40 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 116 optimal weight:    8.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    1.1938

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

Flipped N/Q/H residues before XYZ refinement:
C 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.093730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.080065 restraints weight = 17350.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.07
r_work: 0.3171 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8889
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10304  Z= 0.166
  Angle     :  0.643  21.714  13944  Z= 0.334
  Chirality :  0.047   0.311   1576
  Planarity :  0.008   0.140   1804
  Dihedral  : 10.076 175.715   1412
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.16 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.25), residues: 1328
  helix:  2.17 (0.27), residues: 372
  sheet: -0.38 (0.34), residues: 268
  loop :  0.29 (0.27), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.003   0.000   HIS B 179 
 PHE   0.010   0.001   PHE B 233 
 TYR   0.007   0.001   TYR B 314 
 ARG   0.017   0.001   ARG D 234 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 1.105 
Fit side-chains
  outliers start: 17
  outliers final: 11
  residues processed: 81
  average time/residue: 1.4741
  time to fit residues: 128.0166
Evaluate side-chains
  76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 1.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0770
   chunk 82 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 75 optimal weight:    8.9990
   chunk 71 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 130 optimal weight:    5.9990
   overall best weight:    1.4144

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

Flipped N/Q/H residues before XYZ refinement:
C 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.094609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.080812 restraints weight = 17365.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 2.12
r_work: 0.3182 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8886
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.094  10304  Z= 0.187
  Angle     :  0.753  26.569  13944  Z= 0.384
  Chirality :  0.050   0.454   1576
  Planarity :  0.013   0.275   1804
  Dihedral  :  7.110 177.914   1412
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.98 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.80 (0.25), residues: 1328
  helix:  2.15 (0.27), residues: 372
  sheet: -0.79 (0.34), residues: 264
  loop :  0.29 (0.27), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.011   0.001   HIS D 179 
 PHE   0.012   0.001   PHE D 233 
 TYR   0.009   0.001   TYR B 314 
 ARG   0.046   0.003   ARG A 234 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 63
  time to evaluate  : 1.102 
Fit side-chains
  outliers start: 15
  outliers final: 13
  residues processed: 73
  average time/residue: 1.4396
  time to fit residues: 113.0700
Evaluate side-chains
  73 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 14 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 129 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 97 optimal weight:    7.9990
   chunk 131 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9980
   chunk 92 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
C 264 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.093482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.079564 restraints weight = 17375.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.10
r_work: 0.3159 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8904
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.101  10304  Z= 0.209
  Angle     :  0.724  25.074  13944  Z= 0.371
  Chirality :  0.049   0.421   1576
  Planarity :  0.014   0.318   1804
  Dihedral  :  7.253 178.870   1412
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.98 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.25), residues: 1328
  helix:  2.07 (0.27), residues: 372
  sheet: -0.58 (0.35), residues: 256
  loop :  0.17 (0.27), residues: 700

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.003   0.001   HIS B 179 
 PHE   0.015   0.001   PHE A 233 
 TYR   0.010   0.001   TYR B 314 
 ARG   0.033   0.002   ARG C 234 

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

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

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2656 Ramachandran restraints generated.
    1328 Oldfield, 0 Emsley, 1328 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 1.117 
Fit side-chains
  outliers start: 14
  outliers final: 11
  residues processed: 73
  average time/residue: 1.4546
  time to fit residues: 113.9247
Evaluate side-chains
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  333 SER
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain C residue  333 SER
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  333 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 109 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 108 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 124 optimal weight:    7.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    1.6586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.094085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.080176 restraints weight = 17265.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.13
r_work: 0.3169 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8898
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.093  10304  Z= 0.204
  Angle     :  0.705  23.359  13944  Z= 0.362
  Chirality :  0.049   0.390   1576
  Planarity :  0.014   0.318   1804
  Dihedral  :  5.582  55.274   1412
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.99 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 16.98 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.39 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.25), residues: 1328
  helix:  2.07 (0.27), residues: 372
  sheet: -0.81 (0.34), residues: 264
  loop :  0.27 (0.27), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 313 
 HIS   0.003   0.001   HIS A 179 
 PHE   0.015   0.001   PHE D 233 
 TYR   0.008   0.001   TYR C 314 
 ARG   0.034   0.002   ARG A 234 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7623.29 seconds
wall clock time: 136 minutes 2.28 seconds (8162.28 seconds total)