Starting phenix.real_space_refine
on Sat Aug 23 05:15:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g16_29663/08_2025/8g16_29663.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g16_29663/08_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_29663/08_2025/8g16_29663.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g16_29663/08_2025/8g16_29663.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g16_29663/08_2025/8g16_29663.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g16_29663/08_2025/8g16_29663.cif"
  }
  resolution = 2.07
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.14, per 1000 atoms: 0.21
  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: 0.72
  Conformation dependent library (CDL) restraints added in 326.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.42
  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: 1.56

  Time building geometry restraints manager: 1.01 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: 0.01
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:             0.880
  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:             0.080
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.350
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.230
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.24 (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
 ARG   0.002   0.000   ARG C 323 
 TYR   0.008   0.001   TYR C 314 
 PHE   0.006   0.001   PHE B  11 
 TRP   0.008   0.001   TRP C  87 
 HIS   0.002   0.001   HIS B  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (10304)
  covalent geometry    : angle       0.79288 (13944)
  hydrogen bonds       : bond        0.18717 (  458)
  hydrogen bonds       : angle       7.73919 ( 1305)
  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  : 0.282 
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: 0.5822
  time to fit residues: 64.4356
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  : 0.350 
-------------------------------------------------------------------------------
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 98 optimal weight:    9.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    8.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.3476 r_free = 0.3476 target = 0.089887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.075345 restraints weight = 17010.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.07
r_work: 0.3065 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2952 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8986
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10308  Z= 0.190
  Angle     :  0.563   8.172  13944  Z= 0.312
  Chirality :  0.047   0.143   1576
  Planarity :  0.006   0.070   1804
  Dihedral  :  5.186  30.400   1422
  Min Nonbonded Distance : 2.312

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  3.09 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 15.58 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.24), residues: 1328
  helix:  0.72 (0.25), residues: 372
  sheet:  0.11 (0.37), residues: 204
  loop : -0.47 (0.24), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  80 
 TYR   0.014   0.002   TYR B 314 
 PHE   0.011   0.001   PHE A 318 
 TRP   0.005   0.001   TRP C  87 
 HIS   0.004   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 (10304)
  covalent geometry    : angle       0.56264 (13944)
  hydrogen bonds       : bond        0.05205 (  458)
  hydrogen bonds       : angle       5.91238 ( 1305)
  Misc. bond           : bond        0.00022 (    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
  100 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  142 ASN cc_start: 0.8655 (OUTLIER) cc_final: 0.8381 (t0)
REVERT: B  142 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8374 (t0)
REVERT: C  142 ASN cc_start: 0.8647 (OUTLIER) cc_final: 0.8372 (t0)
REVERT: D  142 ASN cc_start: 0.8640 (OUTLIER) cc_final: 0.8364 (t0)
  outliers start: 25
  outliers final: 4
  residues processed: 89
  average time/residue: 0.6434
  time to fit residues: 60.7086
Evaluate side-chains
  72 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  142 ASN
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 D residue   57 HIS
Chi-restraints excluded: chain D residue  142 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 88 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0970
   chunk 14 optimal weight:    6.9990
   chunk 40 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0040
   chunk 117 optimal weight:    9.9990
   chunk 74 optimal weight:    0.7980
   chunk 123 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   overall best weight:    2.5794

-------------------------------------------------------------------------------
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 = 0.3489 r_free = 0.3489 target = 0.090786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.076155 restraints weight = 17149.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.11
r_work: 0.3078 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8975
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10308  Z= 0.176
  Angle     :  0.649  13.134  13944  Z= 0.341
  Chirality :  0.046   0.134   1576
  Planarity :  0.010   0.192   1804
  Dihedral  :  4.853  29.746   1413
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.12 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.24), residues: 1328
  helix:  1.21 (0.26), residues: 372
  sheet: -0.25 (0.33), residues: 280
  loop : -0.02 (0.26), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  80 
 TYR   0.012   0.001   TYR B 314 
 PHE   0.007   0.001   PHE C 286 
 TRP   0.005   0.001   TRP B 313 
 HIS   0.002   0.000   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (10304)
  covalent geometry    : angle       0.64923 (13944)
  hydrogen bonds       : bond        0.04752 (  458)
  hydrogen bonds       : angle       5.70296 ( 1305)
  Misc. bond           : bond        0.00461 (    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
  95 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 68
  time to evaluate  : 0.416 
Fit side-chains
  outliers start: 27
  outliers final: 12
  residues processed: 81
  average time/residue: 0.6817
  time to fit residues: 58.5593
Evaluate side-chains
  79 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
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  243 VAL
Chi-restraints excluded: chain B residue  318 PHE
Chi-restraints excluded: chain C residue   57 HIS
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  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 39 optimal weight:    0.9980
   chunk 71 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 115 optimal weight:    0.3980
   chunk 65 optimal weight:    3.9990
   chunk 26 optimal weight:    8.9990
   chunk 75 optimal weight:    0.0870
   chunk 85 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    1.4962

-------------------------------------------------------------------------------
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 = 0.3526 r_free = 0.3526 target = 0.093014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.078789 restraints weight = 17186.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3256 rms_B_bonded: 2.11
r_work: 0.3133 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8931
moved from start:          0.1486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  10308  Z= 0.131
  Angle     :  0.556  13.386  13944  Z= 0.302
  Chirality :  0.045   0.217   1576
  Planarity :  0.006   0.103   1804
  Dihedral  : 10.053 169.427   1413
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.56 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.25), residues: 1328
  helix:  1.64 (0.26), residues: 372
  sheet:  0.10 (0.34), residues: 264
  loop :  0.00 (0.26), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 234 
 TYR   0.009   0.001   TYR D 314 
 PHE   0.005   0.001   PHE D 233 
 TRP   0.007   0.001   TRP B 313 
 HIS   0.003   0.000   HIS C 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10304)
  covalent geometry    : angle       0.55585 (13944)
  hydrogen bonds       : bond        0.03821 (  458)
  hydrogen bonds       : angle       5.39491 ( 1305)
  Misc. bond           : bond        0.00691 (    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
  108 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.443 
Fit side-chains
  outliers start: 31
  outliers final: 12
  residues processed: 94
  average time/residue: 0.6682
  time to fit residues: 66.7588
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  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
Chi-restraints excluded: chain A residue  243 VAL
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  243 VAL
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain D residue   57 HIS
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  243 VAL
Chi-restraints excluded: chain D residue  266 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 73 optimal weight:    8.9990
   chunk 26 optimal weight:    5.9990
   chunk 109 optimal weight:    8.9990
   chunk 38 optimal weight:   10.0000
   chunk 113 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    2.1186

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.091022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.076793 restraints weight = 17015.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.09
r_work: 0.3093 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8964
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10308  Z= 0.150
  Angle     :  0.589  11.616  13944  Z= 0.315
  Chirality :  0.046   0.170   1576
  Planarity :  0.005   0.060   1804
  Dihedral  :  4.567  18.423   1412
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.12 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.25), residues: 1328
  helix:  1.70 (0.26), residues: 372
  sheet:  0.00 (0.33), residues: 272
  loop :  0.08 (0.27), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  80 
 TYR   0.010   0.001   TYR B 314 
 PHE   0.006   0.001   PHE D 286 
 TRP   0.007   0.001   TRP B 313 
 HIS   0.002   0.001   HIS D 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10304)
  covalent geometry    : angle       0.58851 (13944)
  hydrogen bonds       : bond        0.04409 (  458)
  hydrogen bonds       : angle       5.44235 ( 1305)
  Misc. bond           : bond        0.00406 (    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
  105 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 72
  time to evaluate  : 0.281 
Fit side-chains
  outliers start: 33
  outliers final: 22
  residues processed: 90
  average time/residue: 0.6734
  time to fit residues: 64.2447
Evaluate side-chains
  88 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
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  244 ASP
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  243 VAL
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain C residue  318 PHE
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 109 optimal weight:    8.9990
   chunk 124 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 43 optimal weight:    8.9990
   chunk 75 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 116 optimal weight:    1.9990
   overall best weight:    1.1786

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.093530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.079561 restraints weight = 17245.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3273 rms_B_bonded: 2.08
r_work: 0.3150 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8912
moved from start:          0.1678

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= 0.104
  Angle     :  0.562  12.816  13944  Z= 0.298
  Chirality :  0.045   0.216   1576
  Planarity :  0.007   0.113   1804
  Dihedral  :  4.458  18.363   1412
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 14.84 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.25), residues: 1328
  helix:  2.04 (0.27), residues: 372
  sheet: -0.04 (0.34), residues: 268
  loop :  0.20 (0.27), residues: 688

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (10304)
  covalent geometry    : angle       0.56176 (13944)
  hydrogen bonds       : bond        0.03545 (  458)
  hydrogen bonds       : angle       5.22959 ( 1305)
  Misc. bond           : bond        0.00471 (    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
  99 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 72
  time to evaluate  : 0.343 
Fit side-chains
  outliers start: 27
  outliers final: 17
  residues processed: 87
  average time/residue: 0.5525
  time to fit residues: 51.4234
Evaluate side-chains
  85 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
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  244 ASP
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  243 VAL
Chi-restraints excluded: chain C residue  266 SER
Chi-restraints excluded: chain C residue  328 MET
Chi-restraints excluded: chain D residue   57 HIS
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0470
   chunk 46 optimal weight:    2.9990
   chunk 109 optimal weight:    8.9990
   chunk 35 optimal weight:    5.9990
   chunk 102 optimal weight:    9.9990
   chunk 24 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0020
   chunk 66 optimal weight:   10.0000
   chunk 97 optimal weight:    5.9990
   overall best weight:    2.0092

-------------------------------------------------------------------------------
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 = 0.3504 r_free = 0.3504 target = 0.091498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.077545 restraints weight = 17161.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.08
r_work: 0.3118 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8940
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10308  Z= 0.162
  Angle     :  0.735  24.241  13944  Z= 0.375
  Chirality :  0.049   0.342   1576
  Planarity :  0.007   0.116   1804
  Dihedral  : 10.185 168.884   1412
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.66 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.77 (0.25), residues: 1328
  helix:  1.92 (0.26), residues: 372
  sheet: -0.22 (0.33), residues: 268
  loop :  0.14 (0.27), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B  80 
 TYR   0.011   0.001   TYR B 314 
 PHE   0.007   0.001   PHE D 233 
 TRP   0.007   0.001   TRP B 313 
 HIS   0.004   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10304)
  covalent geometry    : angle       0.73466 (13944)
  hydrogen bonds       : bond        0.04268 (  458)
  hydrogen bonds       : angle       5.38349 ( 1305)
  Misc. bond           : bond        0.00689 (    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: 28
    poor density    : 66
  time to evaluate  : 0.396 
Fit side-chains
  outliers start: 28
  outliers final: 18
  residues processed: 87
  average time/residue: 0.5924
  time to fit residues: 55.0412
Evaluate side-chains
  80 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
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  244 ASP
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  243 VAL
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 110 optimal weight:    7.9990
   chunk 109 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 76 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 24 optimal weight:   20.0000
   chunk 83 optimal weight:    1.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.091709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.077839 restraints weight = 17250.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.09
r_work: 0.3122 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8935
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      :  0.004   0.044  10308  Z= 0.177
  Angle     :  0.754  18.973  13944  Z= 0.394
  Chirality :  0.054   0.537   1576
  Planarity :  0.020   0.403   1804
  Dihedral  :  8.511 126.093   1412
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 15.03 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.25), residues: 1328
  helix:  1.90 (0.26), residues: 372
  sheet: -0.31 (0.33), residues: 268
  loop :  0.11 (0.26), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.030   0.002   ARG A 234 
 TYR   0.011   0.001   TYR B 314 
 PHE   0.007   0.001   PHE D 318 
 TRP   0.007   0.001   TRP B 313 
 HIS   0.007   0.001   HIS D 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (10304)
  covalent geometry    : angle       0.75422 (13944)
  hydrogen bonds       : bond        0.04441 (  458)
  hydrogen bonds       : angle       5.45007 ( 1305)
  Misc. bond           : bond        0.01349 (    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
  92 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 66
  time to evaluate  : 0.395 
Fit side-chains
  outliers start: 26
  outliers final: 20
  residues processed: 86
  average time/residue: 0.5710
  time to fit residues: 52.5550
Evaluate side-chains
  85 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 65
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
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  244 ASP
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  243 VAL
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   chunk 88 optimal weight:    0.4980
   chunk 99 optimal weight:   10.0000
   chunk 45 optimal weight:    7.9990
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3543 r_free = 0.3543 target = 0.093820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.080195 restraints weight = 17276.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 2.09
r_work: 0.3169 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8891
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10308  Z= 0.111
  Angle     :  0.536  10.450  13944  Z= 0.289
  Chirality :  0.046   0.266   1576
  Planarity :  0.008   0.152   1804
  Dihedral  :  5.138  39.720   1412
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 15.68 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.31 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.89 (0.25), residues: 1328
  helix:  2.17 (0.27), residues: 372
  sheet: -0.54 (0.34), residues: 272
  loop :  0.31 (0.27), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.002   ARG C 234 
 TYR   0.007   0.001   TYR B 314 
 PHE   0.009   0.001   PHE A 233 
 TRP   0.007   0.001   TRP B 313 
 HIS   0.004   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (10304)
  covalent geometry    : angle       0.53612 (13944)
  hydrogen bonds       : bond        0.03556 (  458)
  hydrogen bonds       : angle       5.22755 ( 1305)
  Misc. bond           : bond        0.00426 (    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
  91 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 0.410 
Fit side-chains
  outliers start: 23
  outliers final: 19
  residues processed: 85
  average time/residue: 0.5391
  time to fit residues: 49.4799
Evaluate side-chains
  87 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
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  243 VAL
Chi-restraints excluded: chain B residue  244 ASP
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  243 VAL
Chi-restraints excluded: chain C residue  266 SER
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 85 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 63 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 105 optimal weight:    6.9990
   overall best weight:    2.2986

-------------------------------------------------------------------------------
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 = 0.3503 r_free = 0.3503 target = 0.091473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.077601 restraints weight = 17132.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 2.09
r_work: 0.3117 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8937
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10308  Z= 0.162
  Angle     :  0.607  14.196  13944  Z= 0.325
  Chirality :  0.048   0.314   1576
  Planarity :  0.009   0.160   1804
  Dihedral  :  5.471  43.540   1412
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 15.77 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.62 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.25), residues: 1328
  helix:  1.97 (0.27), residues: 372
  sheet: -0.52 (0.34), residues: 268
  loop :  0.16 (0.27), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.002   ARG B 234 
 TYR   0.011   0.001   TYR B 314 
 PHE   0.012   0.001   PHE A 233 
 TRP   0.006   0.001   TRP B 313 
 HIS   0.005   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (10304)
  covalent geometry    : angle       0.60732 (13944)
  hydrogen bonds       : bond        0.04316 (  458)
  hydrogen bonds       : angle       5.41463 ( 1305)
  Misc. bond           : bond        0.00460 (    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
  84 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.400 
Fit side-chains
  outliers start: 22
  outliers final: 18
  residues processed: 78
  average time/residue: 0.6079
  time to fit residues: 50.8873
Evaluate side-chains
  75 residues out of total 1080 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 57
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 HIS
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  243 VAL
Chi-restraints excluded: chain B residue  244 ASP
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  243 VAL
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  243 VAL
Chi-restraints excluded: chain D residue  266 SER
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 24 optimal weight:   20.0000
   chunk 29 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 2 optimal weight:    3.9990
   chunk 91 optimal weight:    7.9990
   chunk 102 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 28 optimal weight:    0.6980
   chunk 8 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0060
   overall best weight:    2.3402

-------------------------------------------------------------------------------
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 = 0.3499 r_free = 0.3499 target = 0.091194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.077285 restraints weight = 17242.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.10
r_work: 0.3110 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8941
moved from start:          0.1728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10308  Z= 0.164
  Angle     :  0.610  13.850  13944  Z= 0.326
  Chirality :  0.049   0.315   1576
  Planarity :  0.009   0.158   1804
  Dihedral  :  5.516  45.104   1412
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 16.05 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.62 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.25), residues: 1328
  helix:  1.92 (0.27), residues: 372
  sheet: -0.66 (0.34), residues: 272
  loop :  0.19 (0.27), residues: 684

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.002   ARG B 234 
 TYR   0.012   0.001   TYR B 314 
 PHE   0.009   0.001   PHE A 233 
 TRP   0.006   0.001   TRP B 313 
 HIS   0.006   0.001   HIS A 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (10304)
  covalent geometry    : angle       0.61013 (13944)
  hydrogen bonds       : bond        0.04365 (  458)
  hydrogen bonds       : angle       5.42655 ( 1305)
  Misc. bond           : bond        0.00441 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3183.15 seconds
wall clock time: 55 minutes 4.51 seconds (3304.51 seconds total)