Starting phenix.real_space_refine
on Wed Apr 30 21:28:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g16_29663/04_2025/8g16_29663.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g16_29663/04_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_29663/04_2025/8g16_29663.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g16_29663/04_2025/8g16_29663.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g16_29663/04_2025/8g16_29663.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g16_29663/04_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-5669/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: 5.95, per 1000 atoms: 0.59
  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: 2.32
  Conformation dependent library (CDL) restraints added in 1.1 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: 1.21
  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: 3.01

  Time building geometry restraints manager: 2.76 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:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.300
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     24.720
  Find NCS groups from input model:        0.320
  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:12.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.260
-------------------------------------------------------------------------------
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      :  0.014   0.664  10308  Z= 1.318
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18717 (  458)
  hydrogen bonds       : angle       7.73919 ( 1305)
  covalent geometry    : bond        0.00420 (10304)
  covalent geometry    : angle       0.79288 (13944)
  Misc. bond           : bond        0.65587 (    4)

*********************** 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  : 1.054 
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: 1.4954
  time to fit residues: 165.8487
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  : 1.063 
-------------------------------------------------------------------------------
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 = 16811.032|
|-----------------------------------------------------------------------------|
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  10308  Z= 0.230
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05655 (  458)
  hydrogen bonds       : angle       6.04308 ( 1305)
  covalent geometry    : bond        0.00543 (10304)
  covalent geometry    : angle       0.59857 (13944)
  Misc. bond           : bond        0.00122 (    4)

*********************** 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  : 1.162 
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: 0.8397 (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: 1.5814
  time to fit residues: 153.1816
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  : 1.364 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 108 optimal weight:    8.9990
   chunk 101 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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 = 0.3435 r_free = 0.3435 target = 0.087776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.073438 restraints weight = 17267.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 2.07
r_work: 0.3031 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9003
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088  10308  Z= 0.283
  Angle     :  0.691  14.741  13944  Z= 0.375
  Chirality :  0.050   0.161   1576
  Planarity :  0.008   0.201   1804
  Dihedral  :  5.361  34.520   1416
  Min Nonbonded Distance : 2.223

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:  0.02 (0.24), residues: 1328
  helix:  0.92 (0.26), residues: 364
  sheet: -0.01 (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 D 179 
 PHE   0.011   0.002   PHE D 286 
 TYR   0.015   0.002   TYR D 314 
 ARG   0.008   0.001   ARG B 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05986 (  458)
  hydrogen bonds       : angle       6.04186 ( 1305)
  covalent geometry    : bond        0.00682 (10304)
  covalent geometry    : angle       0.69080 (13944)
  Misc. bond           : bond        0.00298 (    4)

*********************** 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
  106 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 68
  time to evaluate  : 1.075 
Fit side-chains
REVERT: A  142 ASN cc_start: 0.8762 (OUTLIER) cc_final: 0.8449 (t0)
REVERT: B  142 ASN cc_start: 0.8761 (OUTLIER) cc_final: 0.8446 (t0)
REVERT: C  142 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8451 (t0)
REVERT: D  142 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8457 (t0)
  outliers start: 38
  outliers final: 16
  residues processed: 90
  average time/residue: 1.6352
  time to fit residues: 156.1626
Evaluate side-chains
  90 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 70
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
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  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:    7.9990
   chunk 23 optimal weight:    0.3980
   chunk 93 optimal weight:    0.3980
   chunk 117 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 31 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0970
   chunk 87 optimal weight:   10.0000
   chunk 27 optimal weight:    6.9990
   overall best weight:    1.9782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.090248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.076225 restraints weight = 17127.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 2.07
r_work: 0.3090 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8963
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10308  Z= 0.147
  Angle     :  0.626  14.783  13944  Z= 0.330
  Chirality :  0.045   0.236   1576
  Planarity :  0.009   0.173   1804
  Dihedral  :  6.671 167.626   1416
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.31 %
    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:  0.45 (0.24), residues: 1328
  helix:  1.33 (0.26), residues: 372
  sheet: -0.05 (0.33), residues: 272
  loop : -0.02 (0.27), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 313 
 HIS   0.002   0.000   HIS D 137 
 PHE   0.009   0.001   PHE B 233 
 TYR   0.009   0.001   TYR D 314 
 ARG   0.019   0.002   ARG A 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04308 (  458)
  hydrogen bonds       : angle       5.57938 ( 1305)
  covalent geometry    : bond        0.00343 (10304)
  covalent geometry    : angle       0.62585 (13944)
  Misc. bond           : bond        0.00488 (    4)

*********************** 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
  103 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 70
  time to evaluate  : 1.586 
Fit side-chains
REVERT: A  142 ASN cc_start: 0.8683 (OUTLIER) cc_final: 0.8444 (t0)
REVERT: B  142 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8444 (t0)
REVERT: C  142 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8442 (t0)
REVERT: D  142 ASN cc_start: 0.8679 (OUTLIER) cc_final: 0.8437 (t0)
  outliers start: 33
  outliers final: 17
  residues processed: 93
  average time/residue: 1.9702
  time to fit residues: 194.6093
Evaluate side-chains
  84 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 63
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
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  328 MET
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  333 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 59 optimal weight:    4.9990
   chunk 122 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    4.3990

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.087933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.073724 restraints weight = 17247.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.06
r_work: 0.3037 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9003
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.080  10308  Z= 0.270
  Angle     :  0.728  19.161  13944  Z= 0.393
  Chirality :  0.051   0.290   1576
  Planarity :  0.007   0.104   1804
  Dihedral  :  9.411 169.147   1416
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 14.94 %
    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:  0.40 (0.24), residues: 1328
  helix:  1.21 (0.26), residues: 364
  sheet: -0.00 (0.34), residues: 272
  loop : -0.04 (0.26), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 313 
 HIS   0.004   0.001   HIS B 179 
 PHE   0.010   0.002   PHE C 286 
 TYR   0.013   0.002   TYR C 314 
 ARG   0.013   0.001   ARG C 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05699 (  458)
  hydrogen bonds       : angle       5.92513 ( 1305)
  covalent geometry    : bond        0.00647 (10304)
  covalent geometry    : angle       0.72754 (13944)
  Misc. bond           : bond        0.00721 (    4)

*********************** 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
  113 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 72
  time to evaluate  : 1.203 
Fit side-chains
REVERT: A  142 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8489 (t0)
REVERT: B  142 ASN cc_start: 0.8791 (OUTLIER) cc_final: 0.8486 (t0)
REVERT: C  142 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8487 (t0)
REVERT: D  142 ASN cc_start: 0.8795 (OUTLIER) cc_final: 0.8484 (t0)
  outliers start: 41
  outliers final: 19
  residues processed: 98
  average time/residue: 1.5568
  time to fit residues: 162.7332
Evaluate side-chains
  89 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 1.512 
-------------------------------------------------------------------------------
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  203 LEU
Chi-restraints excluded: chain A residue  243 VAL
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  243 VAL
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  203 LEU
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  203 LEU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
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:   20.0000
   chunk 126 optimal weight:    0.0370
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 70 optimal weight:    5.9990
   chunk 96 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.1862

-------------------------------------------------------------------------------
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 = 0.3525 r_free = 0.3525 target = 0.092793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.079040 restraints weight = 17099.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.09
r_work: 0.3147 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8918
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.104  10308  Z= 0.129
  Angle     :  0.587  14.286  13944  Z= 0.318
  Chirality :  0.044   0.182   1576
  Planarity :  0.006   0.096   1804
  Dihedral  :  9.396 175.260   1416
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  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:  0.73 (0.25), residues: 1328
  helix:  1.71 (0.26), residues: 372
  sheet:  0.08 (0.34), residues: 264
  loop :  0.07 (0.27), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 313 
 HIS   0.005   0.001   HIS A 179 
 PHE   0.006   0.001   PHE B 233 
 TYR   0.006   0.001   TYR B 314 
 ARG   0.012   0.001   ARG B  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03842 (  458)
  hydrogen bonds       : angle       5.46443 ( 1305)
  covalent geometry    : bond        0.00299 (10304)
  covalent geometry    : angle       0.58745 (13944)
  Misc. bond           : bond        0.00803 (    4)

*********************** 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
  98 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 73
  time to evaluate  : 1.111 
Fit side-chains
  outliers start: 25
  outliers final: 12
  residues processed: 93
  average time/residue: 1.5727
  time to fit residues: 155.7000
Evaluate side-chains
  77 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 1.086 
-------------------------------------------------------------------------------
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  243 VAL
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  333 SER
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  243 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 122 optimal weight:    0.8980
   chunk 1 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 72 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 109 optimal weight:    8.9990
   chunk 101 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 62 optimal weight:    6.9990
   chunk 112 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.0786

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

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

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.090276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.076162 restraints weight = 17324.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 2.10
r_work: 0.3087 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8962
moved from start:          0.1709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10308  Z= 0.152
  Angle     :  0.631  22.311  13944  Z= 0.335
  Chirality :  0.047   0.330   1576
  Planarity :  0.006   0.128   1804
  Dihedral  :  6.594 166.125   1415
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.14 %
    Favored  : 81.45 %
  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:  0.66 (0.25), residues: 1328
  helix:  1.67 (0.26), residues: 372
  sheet: -0.10 (0.33), residues: 272
  loop :  0.09 (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 B 179 
 PHE   0.007   0.001   PHE B 233 
 TYR   0.011   0.001   TYR B 314 
 ARG   0.013   0.001   ARG B 234 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04365 (  458)
  hydrogen bonds       : angle       5.44908 ( 1305)
  covalent geometry    : bond        0.00342 (10304)
  covalent geometry    : angle       0.63146 (13944)
  Misc. bond           : bond        0.00506 (    4)

*********************** 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
  94 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 68
  time to evaluate  : 1.078 
Fit side-chains
  outliers start: 26
  outliers final: 17
  residues processed: 84
  average time/residue: 1.5020
  time to fit residues: 134.5033
Evaluate side-chains
  80 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
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  243 VAL
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  195 LEU
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   57 HIS
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  243 VAL
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain C residue  318 PHE
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  318 PHE
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:    7.9990
   chunk 52 optimal weight:    0.0370
   chunk 18 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 85 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 116 optimal weight:    6.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    1.1662

-------------------------------------------------------------------------------
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 = 0.3535 r_free = 0.3535 target = 0.093619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.079948 restraints weight = 17372.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.07
r_work: 0.3169 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3058 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3058
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8892
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   0.046  10308  Z= 0.115
  Angle     :  0.560  14.045  13944  Z= 0.300
  Chirality :  0.046   0.241   1576
  Planarity :  0.007   0.119   1804
  Dihedral  : 10.178 174.782   1415
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.42 %
    Favored  : 81.54 %
  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:  0.85 (0.25), residues: 1328
  helix:  2.05 (0.27), residues: 372
  sheet: -0.37 (0.34), residues: 268
  loop :  0.24 (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   0.014   0.001   ARG D  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03468 (  458)
  hydrogen bonds       : angle       5.27447 ( 1305)
  covalent geometry    : bond        0.00253 (10304)
  covalent geometry    : angle       0.55957 (13944)
  Misc. bond           : bond        0.00643 (    4)

*********************** 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
  91 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 2.050 
Fit side-chains
  outliers start: 22
  outliers final: 14
  residues processed: 86
  average time/residue: 1.8779
  time to fit residues: 172.9573
Evaluate side-chains
  76 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
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  243 VAL
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  195 LEU
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 20 optimal weight:    0.3980
   chunk 26 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0030
   chunk 75 optimal weight:    0.0010
   chunk 71 optimal weight:   10.0000
   chunk 17 optimal weight:    0.8980
   chunk 130 optimal weight:    8.9990
   overall best weight:    0.4598

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.097362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.083979 restraints weight = 17447.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 2.08
r_work: 0.3247 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3137 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10308  Z= 0.085
  Angle     :  0.474   5.828  13944  Z= 0.258
  Chirality :  0.044   0.168   1576
  Planarity :  0.006   0.074   1804
  Dihedral  : 10.401 178.655   1412
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 17.72 %
    Favored  : 81.54 %
  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:  1.12 (0.26), residues: 1328
  helix:  2.47 (0.27), residues: 372
  sheet: -0.20 (0.36), residues: 240
  loop :  0.24 (0.27), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 313 
 HIS   0.002   0.000   HIS D 179 
 PHE   0.009   0.001   PHE D 233 
 TYR   0.006   0.001   TYR B 276 
 ARG   0.015   0.001   ARG D  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02810 (  458)
  hydrogen bonds       : angle       5.06454 ( 1305)
  covalent geometry    : bond        0.00178 (10304)
  covalent geometry    : angle       0.47443 (13944)
  Misc. bond           : bond        0.00442 (    4)

*********************** 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: 8
    poor density    : 70
  time to evaluate  : 1.062 
Fit side-chains
  outliers start: 8
  outliers final: 8
  residues processed: 73
  average time/residue: 1.3847
  time to fit residues: 108.6147
Evaluate side-chains
  74 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 66
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  244 ASP
Chi-restraints excluded: chain C residue   57 HIS
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 105 optimal weight:    5.9990
   chunk 14 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 129 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 97 optimal weight:    4.9990
   chunk 131 optimal weight:    4.9990
   chunk 89 optimal weight:    0.9990
   chunk 92 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.091984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.078014 restraints weight = 17424.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.11
r_work: 0.3127 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8933
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10308  Z= 0.151
  Angle     :  0.558   8.401  13944  Z= 0.308
  Chirality :  0.047   0.276   1576
  Planarity :  0.006   0.076   1804
  Dihedral  : 10.721 178.579   1412
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 17.07 %
    Favored  : 81.82 %
  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:  0.89 (0.25), residues: 1328
  helix:  2.13 (0.27), residues: 372
  sheet: -0.46 (0.34), residues: 268
  loop :  0.29 (0.27), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 313 
 HIS   0.003   0.001   HIS B 179 
 PHE   0.008   0.001   PHE A 233 
 TYR   0.010   0.001   TYR B 314 
 ARG   0.015   0.001   ARG C  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04127 (  458)
  hydrogen bonds       : angle       5.32395 ( 1305)
  covalent geometry    : bond        0.00341 (10304)
  covalent geometry    : angle       0.55772 (13944)
  Misc. bond           : bond        0.00569 (    4)

********************** 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
  74 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 1.362 
Fit side-chains
  outliers start: 12
  outliers final: 11
  residues processed: 69
  average time/residue: 1.4797
  time to fit residues: 109.9779
Evaluate side-chains
  70 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  195 LEU
Chi-restraints excluded: chain B residue   57 HIS
Chi-restraints excluded: chain B residue  195 LEU
Chi-restraints excluded: chain B residue  243 VAL
Chi-restraints excluded: chain B residue  244 ASP
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  333 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 109 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   chunk 84 optimal weight:    7.9990
   chunk 108 optimal weight:    7.9990
   chunk 81 optimal weight:    0.3980
   chunk 30 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 124 optimal weight:    0.0030
   chunk 86 optimal weight:    0.0670
   overall best weight:    0.7730

-------------------------------------------------------------------------------
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 = 0.3564 r_free = 0.3564 target = 0.095377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.081698 restraints weight = 17381.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.09
r_work: 0.3209 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8864
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10308  Z= 0.089
  Angle     :  0.471   5.552  13944  Z= 0.257
  Chirality :  0.044   0.179   1576
  Planarity :  0.006   0.071   1804
  Dihedral  : 10.539 178.899   1412
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 17.07 %
    Favored  : 81.82 %
  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:  1.04 (0.26), residues: 1328
  helix:  2.42 (0.27), residues: 372
  sheet: -0.95 (0.33), residues: 284
  loop :  0.61 (0.28), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 313 
 HIS   0.002   0.000   HIS C 137 
 PHE   0.006   0.001   PHE A 233 
 TYR   0.006   0.001   TYR B 314 
 ARG   0.015   0.001   ARG B  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03016 (  458)
  hydrogen bonds       : angle       5.04365 ( 1305)
  covalent geometry    : bond        0.00191 (10304)
  covalent geometry    : angle       0.47070 (13944)
  Misc. bond           : bond        0.00359 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8223.94 seconds
wall clock time: 144 minutes 7.00 seconds (8647.00 seconds total)