Starting phenix.real_space_refine (version: 1.21rc1)
on Sun Apr 23 02:28:15 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/04_2023/7oo8_13007.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/04_2023/7oo8_13007.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/04_2023/7oo8_13007.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/04_2023/7oo8_13007.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/04_2023/7oo8_13007.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oo8_13007/04_2023/7oo8_13007.pdb"
  }
  resolution = 3.7
  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
-------------------------------------------------------------------------------
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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    8932      2.51       5
     N    2436      2.21       5
     O    2513      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 13923
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "B"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "C"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "D"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "E"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "F"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
    Chain: "G"
      Number of atoms: 1989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1989
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 5, 'TRANS': 255}
  Time building chain proxies: 7.24, per 1000 atoms: 0.52
  Number of scatterers: 13923
  At special positions: 0
  Unit cell: (98.9055, 98.9055, 141.446, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    2513      8.00
     N    2436      7.00
     C    8932      6.00
    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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.78
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3374

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 9 sheets defined
      55.9% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 59
      removed outlier: 3.508A  pdb=" N   ARG A  59 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 90
    Processing helix  chain 'A' and resid 93 through 128
      removed outlier: 4.700A  pdb=" N   GLY A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER A 114 " --> pdb=" O   ALA A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 197 through 212
    Processing helix  chain 'A' and resid 245 through 265
    Processing helix  chain 'B' and resid 22 through 59
      removed outlier: 3.508A  pdb=" N   ARG B  59 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 62 through 90
    Processing helix  chain 'B' and resid 93 through 128
      removed outlier: 4.700A  pdb=" N   GLY B 113 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER B 114 " --> pdb=" O   ALA B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 172
    Processing helix  chain 'B' and resid 197 through 212
    Processing helix  chain 'B' and resid 245 through 265
    Processing helix  chain 'C' and resid 22 through 59
      removed outlier: 3.508A  pdb=" N   ARG C  59 " --> pdb=" O   LEU C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 62 through 90
    Processing helix  chain 'C' and resid 93 through 128
      removed outlier: 4.700A  pdb=" N   GLY C 113 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER C 114 " --> pdb=" O   ALA C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 167 through 172
    Processing helix  chain 'C' and resid 197 through 212
    Processing helix  chain 'C' and resid 245 through 265
    Processing helix  chain 'D' and resid 22 through 59
      removed outlier: 3.509A  pdb=" N   ARG D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 90
    Processing helix  chain 'D' and resid 93 through 128
      removed outlier: 4.700A  pdb=" N   GLY D 113 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER D 114 " --> pdb=" O   ALA D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 167 through 172
    Processing helix  chain 'D' and resid 197 through 212
    Processing helix  chain 'D' and resid 245 through 265
    Processing helix  chain 'E' and resid 22 through 59
      removed outlier: 3.509A  pdb=" N   ARG E  59 " --> pdb=" O   LEU E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 62 through 90
    Processing helix  chain 'E' and resid 93 through 128
      removed outlier: 4.701A  pdb=" N   GLY E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER E 114 " --> pdb=" O   ALA E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 167 through 172
    Processing helix  chain 'E' and resid 197 through 212
    Processing helix  chain 'E' and resid 245 through 265
    Processing helix  chain 'F' and resid 22 through 59
      removed outlier: 3.509A  pdb=" N   ARG F  59 " --> pdb=" O   LEU F  55 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 62 through 90
    Processing helix  chain 'F' and resid 93 through 128
      removed outlier: 4.699A  pdb=" N   GLY F 113 " --> pdb=" O   LEU F 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER F 114 " --> pdb=" O   ALA F 110 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 167 through 172
    Processing helix  chain 'F' and resid 197 through 212
    Processing helix  chain 'F' and resid 245 through 265
    Processing helix  chain 'G' and resid 22 through 59
      removed outlier: 3.509A  pdb=" N   ARG G  59 " --> pdb=" O   LEU G  55 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 62 through 90
    Processing helix  chain 'G' and resid 93 through 128
      removed outlier: 4.699A  pdb=" N   GLY G 113 " --> pdb=" O   LEU G 109 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   SER G 114 " --> pdb=" O   ALA G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 167 through 172
    Processing helix  chain 'G' and resid 197 through 212
    Processing helix  chain 'G' and resid 245 through 265
    Processing sheet with id=AA1, first strand: chain 'A' and resid 135 through 138
      removed outlier: 3.679A  pdb=" N   VAL A 141 " --> pdb=" O   LEU A 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR A 154 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   SER A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL G 141 " --> pdb=" O   LEU G 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR G 154 " --> pdb=" O   LEU G 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL G 148 " --> pdb=" O   SER G 152 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   SER G 152 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL F 141 " --> pdb=" O   LEU F 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR F 154 " --> pdb=" O   LEU F 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL F 148 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL E 141 " --> pdb=" O   LEU E 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR E 154 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL E 148 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   SER E 152 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL D 141 " --> pdb=" O   LEU D 138 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   THR D 154 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL D 148 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   SER D 152 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   VAL C 141 " --> pdb=" O   LEU C 138 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   THR C 154 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.371A  pdb=" N   VAL C 148 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   SER C 152 " --> pdb=" O   VAL C 148 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   VAL B 141 " --> pdb=" O   LEU B 138 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   THR B 154 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   SER B 152 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 192
      removed outlier: 6.808A  pdb=" N   ASN A 234 " --> pdb=" O   ASN A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278
      removed outlier: 8.288A  pdb=" N   MET B 273 " --> pdb=" O   GLN A 272 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ASP A 274 " --> pdb=" O   MET B 273 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   VAL B 275 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   ASN A 276 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 8.367A  pdb=" N   MET C 273 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   ASP B 274 " --> pdb=" O   MET C 273 " (cutoff:3.500A)
      removed outlier: 7.024A  pdb=" N   VAL C 275 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   ASN B 276 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   PHE C 277 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   MET D 273 " --> pdb=" O   GLN C 272 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP C 274 " --> pdb=" O   MET D 273 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   VAL D 275 " --> pdb=" O   ASP C 274 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   ASN C 276 " --> pdb=" O   VAL D 275 " (cutoff:3.500A)
      removed outlier: 7.481A  pdb=" N   PHE D 277 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)
      removed outlier: 7.493A  pdb=" N   LYS C 278 " --> pdb=" O   PHE D 277 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   MET E 273 " --> pdb=" O   GLN D 272 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ASP D 274 " --> pdb=" O   MET E 273 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   VAL E 275 " --> pdb=" O   ASP D 274 " (cutoff:3.500A)
      removed outlier: 6.032A  pdb=" N   ASN D 276 " --> pdb=" O   VAL E 275 " (cutoff:3.500A)
      removed outlier: 7.564A  pdb=" N   PHE E 277 " --> pdb=" O   ASN D 276 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   LYS D 278 " --> pdb=" O   PHE E 277 " (cutoff:3.500A)
      removed outlier: 8.306A  pdb=" N   MET F 273 " --> pdb=" O   GLN E 272 " (cutoff:3.500A)
      removed outlier: 6.182A  pdb=" N   ASP E 274 " --> pdb=" O   MET F 273 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   VAL F 275 " --> pdb=" O   ASP E 274 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ASN E 276 " --> pdb=" O   VAL F 275 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE F 277 " --> pdb=" O   ASN E 276 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   LYS E 278 " --> pdb=" O   PHE F 277 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   MET G 273 " --> pdb=" O   GLN F 272 " (cutoff:3.500A)
      removed outlier: 6.148A  pdb=" N   ASP F 274 " --> pdb=" O   MET G 273 " (cutoff:3.500A)
      removed outlier: 7.150A  pdb=" N   VAL G 275 " --> pdb=" O   ASP F 274 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   ASN F 276 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
      removed outlier: 7.494A  pdb=" N   PHE G 277 " --> pdb=" O   ASN F 276 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   LYS F 278 " --> pdb=" O   PHE G 277 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 183 through 192
      removed outlier: 6.809A  pdb=" N   ASN B 234 " --> pdb=" O   ASN B 226 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 192
      removed outlier: 6.809A  pdb=" N   ASN C 234 " --> pdb=" O   ASN C 226 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 183 through 192
      removed outlier: 6.808A  pdb=" N   ASN D 234 " --> pdb=" O   ASN D 226 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 183 through 192
      removed outlier: 6.808A  pdb=" N   ASN E 234 " --> pdb=" O   ASN E 226 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 183 through 192
      removed outlier: 6.809A  pdb=" N   ASN F 234 " --> pdb=" O   ASN F 226 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'G' and resid 183 through 192
      removed outlier: 6.808A  pdb=" N   ASN G 234 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)

    1055 hydrogen bonds defined for protein.
    3081 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: 4.24

  Time building geometry restraints manager: 6.15 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 4654
        1.34 -     1.46: 2133
        1.46 -     1.57: 7227
        1.57 -     1.69: 0
        1.69 -     1.80: 84
  Bond restraints: 14098
  Sorted by residual:
  bond pdb=" C   ARG C 128 "
       pdb=" O   ARG C 128 "
    ideal  model  delta    sigma   weight residual
    1.235  1.231  0.003 4.70e-03 4.53e+04 5.50e-01
  bond pdb=" C   ARG G 128 "
       pdb=" O   ARG G 128 "
    ideal  model  delta    sigma   weight residual
    1.235  1.232  0.003 4.70e-03 4.53e+04 4.64e-01
  bond pdb=" C   ARG E 128 "
       pdb=" O   ARG E 128 "
    ideal  model  delta    sigma   weight residual
    1.235  1.232  0.003 4.70e-03 4.53e+04 4.48e-01
  bond pdb=" N   ILE D 165 "
       pdb=" CA  ILE D 165 "
    ideal  model  delta    sigma   weight residual
    1.460  1.454  0.006 9.30e-03 1.16e+04 4.42e-01
  bond pdb=" C   ARG F 128 "
       pdb=" O   ARG F 128 "
    ideal  model  delta    sigma   weight residual
    1.235  1.232  0.003 4.70e-03 4.53e+04 4.12e-01
  ... (remaining 14093 not shown)

  Histogram of bond angle deviations from ideal:
      100.64 -   107.30: 237
      107.30 -   113.96: 8450
      113.96 -   120.63: 5556
      120.63 -   127.29: 4811
      127.29 -   133.95: 63
  Bond angle restraints: 19117
  Sorted by residual:
  angle pdb=" N   ILE B  83 "
        pdb=" CA  ILE B  83 "
        pdb=" CB  ILE B  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.99   -3.22 1.81e+00 3.05e-01 3.16e+00
  angle pdb=" N   ILE D  83 "
        pdb=" CA  ILE D  83 "
        pdb=" CB  ILE D  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.96   -3.19 1.81e+00 3.05e-01 3.12e+00
  angle pdb=" N   ILE C  83 "
        pdb=" CA  ILE C  83 "
        pdb=" CB  ILE C  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.95   -3.18 1.81e+00 3.05e-01 3.08e+00
  angle pdb=" N   ILE E  83 "
        pdb=" CA  ILE E  83 "
        pdb=" CB  ILE E  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.91   -3.14 1.81e+00 3.05e-01 3.02e+00
  angle pdb=" N   ILE F  83 "
        pdb=" CA  ILE F  83 "
        pdb=" CB  ILE F  83 "
      ideal   model   delta    sigma   weight residual
     110.77  113.91   -3.14 1.81e+00 3.05e-01 3.00e+00
  ... (remaining 19112 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.84: 7336
        9.84 -    19.68: 805
       19.68 -    29.51: 238
       29.51 -    39.35: 91
       39.35 -    49.19: 14
  Dihedral angle restraints: 8484
    sinusoidal: 3248
      harmonic: 5236
  Sorted by residual:
  dihedral pdb=" C   ILE C  83 "
           pdb=" N   ILE C  83 "
           pdb=" CA  ILE C  83 "
           pdb=" CB  ILE C  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.26    8.26     0      2.50e+00 1.60e-01 1.09e+01
  dihedral pdb=" C   ILE A  83 "
           pdb=" N   ILE A  83 "
           pdb=" CA  ILE A  83 "
           pdb=" CB  ILE A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.24    8.24     0      2.50e+00 1.60e-01 1.09e+01
  dihedral pdb=" C   ILE B  83 "
           pdb=" N   ILE B  83 "
           pdb=" CA  ILE B  83 "
           pdb=" CB  ILE B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -130.22    8.22     0      2.50e+00 1.60e-01 1.08e+01
  ... (remaining 8481 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1774
       0.042 -    0.083: 410
       0.083 -    0.125: 140
       0.125 -    0.166: 14
       0.166 -    0.208: 7
  Chirality restraints: 2345
  Sorted by residual:
  chirality pdb=" CA  ILE C  83 "
            pdb=" N   ILE C  83 "
            pdb=" C   ILE C  83 "
            pdb=" CB  ILE C  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  ILE B  83 "
            pdb=" N   ILE B  83 "
            pdb=" C   ILE B  83 "
            pdb=" CB  ILE B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ILE A  83 "
            pdb=" N   ILE A  83 "
            pdb=" C   ILE A  83 "
            pdb=" CB  ILE A  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.23    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 2342 not shown)

  Planarity restraints: 2429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL G 275 "    0.004 2.00e-02 2.50e+03   7.56e-03 5.71e-01
        pdb=" C   VAL G 275 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   VAL G 275 "    0.005 2.00e-02 2.50e+03
        pdb=" N   ASN G 276 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL D 275 "    0.004 2.00e-02 2.50e+03   7.54e-03 5.69e-01
        pdb=" C   VAL D 275 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   VAL D 275 "    0.005 2.00e-02 2.50e+03
        pdb=" N   ASN D 276 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 275 "    0.004 2.00e-02 2.50e+03   7.52e-03 5.65e-01
        pdb=" C   VAL E 275 "   -0.013 2.00e-02 2.50e+03
        pdb=" O   VAL E 275 "    0.005 2.00e-02 2.50e+03
        pdb=" N   ASN E 276 "    0.004 2.00e-02 2.50e+03
  ... (remaining 2426 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3570
        2.81 -     3.33: 14071
        3.33 -     3.85: 23177
        3.85 -     4.38: 25652
        4.38 -     4.90: 45696
  Nonbonded interactions: 112166
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 202 "
            pdb=" OE1 GLU C 255 "
     model   vdw
     2.286 2.520
  nonbonded pdb=" NH2 ARG E  88 "
            pdb=" O   GLY F  90 "
     model   vdw
     2.291 2.520
  nonbonded pdb=" NH2 ARG D  88 "
            pdb=" O   GLY E  90 "
     model   vdw
     2.292 2.520
  nonbonded pdb=" NH2 ARG C  88 "
            pdb=" O   GLY D  90 "
     model   vdw
     2.293 2.520
  nonbonded pdb=" NH2 ARG F  88 "
            pdb=" O   GLY G  90 "
     model   vdw
     2.310 2.520
  ... (remaining 112161 not shown)

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

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 group one per residue
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:             1.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          7.170
  Check model and map are aligned:         0.210
  Set scattering table:                    0.130
  Process input model:                     36.940
  Find NCS groups from input model:        0.920
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.017  14098  Z= 0.185
  Angle     :  0.399   4.564  19117  Z= 0.228
  Chirality :  0.041   0.208   2345
  Planarity :  0.002   0.018   2429
  Dihedral  :  9.895  49.189   5110
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.19), residues: 1813
  helix:  3.46 (0.15), residues: 1008
  sheet:  0.09 (0.28), residues: 294
  loop : -0.47 (0.25), residues: 511

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  426 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 426
  time to evaluate  : 1.619 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 426
  average time/residue: 0.2491
  time to fit residues: 154.2395
Evaluate side-chains
  311 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 311
  time to evaluate  : 1.816 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 2.5137
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 153 optimal weight:    4.9990
   chunk 137 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 142 optimal weight:    2.9990
   chunk 55 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   chunk 165 optimal weight:    3.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
B 247 GLN
D 149 GLN
E 247 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.056  14098  Z= 0.251
  Angle     :  0.475   4.802  19117  Z= 0.261
  Chirality :  0.042   0.176   2345
  Planarity :  0.003   0.033   2429
  Dihedral  :  3.893  12.890   1988
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer Outliers :  2.64 %
  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:  2.56 (0.19), residues: 1813
  helix:  3.24 (0.14), residues: 1008
  sheet: -0.07 (0.27), residues: 294
  loop : -0.44 (0.26), residues: 511

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  372 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 333
  time to evaluate  : 1.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 39
  outliers final: 26
  residues processed: 338
  average time/residue: 0.2261
  time to fit residues: 115.4455
Evaluate side-chains
  311 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 285
  time to evaluate  : 1.748 
Switching outliers to nearest non-outliers
  outliers start: 26
  outliers final: 0
  residues processed: 26
  average time/residue: 0.1249
  time to fit residues: 8.3805
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 137 optimal weight:    2.9990
   chunk 112 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 165 optimal weight:    6.9990
   chunk 178 optimal weight:    2.9990
   chunk 147 optimal weight:    3.9990
   chunk 164 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 132 optimal weight:    0.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14098  Z= 0.246
  Angle     :  0.454   4.724  19117  Z= 0.250
  Chirality :  0.041   0.141   2345
  Planarity :  0.003   0.030   2429
  Dihedral  :  3.934  13.139   1988
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer Outliers :  1.83 %
  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:  2.54 (0.19), residues: 1813
  helix:  3.13 (0.15), residues: 1015
  sheet:  0.57 (0.29), residues: 259
  loop : -0.67 (0.26), residues: 539

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 304
  time to evaluate  : 1.624 
Fit side-chains
   revert: symmetry clash
  outliers start: 27
  outliers final: 18
  residues processed: 314
  average time/residue: 0.2201
  time to fit residues: 105.9286
Evaluate side-chains
  295 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 277
  time to evaluate  : 1.686 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 0
  residues processed: 18
  average time/residue: 0.1293
  time to fit residues: 6.5404
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 163 optimal weight:    0.5980
   chunk 124 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 18 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 111 optimal weight:    2.9990
   chunk 166 optimal weight:    2.9990
   chunk 175 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 157 optimal weight:    0.9980
   chunk 47 optimal weight:    7.9990
   overall best weight:    1.2182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032  14098  Z= 0.175
  Angle     :  0.424   4.996  19117  Z= 0.234
  Chirality :  0.041   0.142   2345
  Planarity :  0.003   0.044   2429
  Dihedral  :  3.867  13.828   1988
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer Outliers :  2.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.68 (0.19), residues: 1813
  helix:  3.27 (0.15), residues: 1015
  sheet:  0.70 (0.28), residues: 273
  loop : -0.77 (0.26), residues: 525

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 319
  time to evaluate  : 1.782 
Fit side-chains
   revert: symmetry clash
  outliers start: 31
  outliers final: 14
  residues processed: 332
  average time/residue: 0.2170
  time to fit residues: 110.6990
Evaluate side-chains
  308 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 294
  time to evaluate  : 1.719 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 0
  residues processed: 14
  average time/residue: 0.1214
  time to fit residues: 5.5469
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 146 optimal weight:    4.9990
   chunk 99 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 130 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 150 optimal weight:    3.9990
   chunk 121 optimal weight:    4.9990
   chunk 0 optimal weight:   10.0000
   chunk 89 optimal weight:    3.9990
   chunk 157 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    1.4986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14098  Z= 0.200
  Angle     :  0.434   5.153  19117  Z= 0.238
  Chirality :  0.041   0.144   2345
  Planarity :  0.003   0.043   2429
  Dihedral  :  3.876  15.211   1988
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer Outliers :  1.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.19), residues: 1813
  helix:  3.18 (0.15), residues: 1015
  sheet:  0.75 (0.29), residues: 259
  loop : -0.68 (0.26), residues: 539

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 302
  time to evaluate  : 1.800 
Fit side-chains
  outliers start: 23
  outliers final: 16
  residues processed: 313
  average time/residue: 0.2146
  time to fit residues: 103.9653
Evaluate side-chains
  304 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 288
  time to evaluate  : 1.756 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 0
  residues processed: 16
  average time/residue: 0.1215
  time to fit residues: 6.0337
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 158 optimal weight:    0.6980
   chunk 34 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 176 optimal weight:    2.9990
   chunk 146 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 58 optimal weight:    5.9990
   chunk 92 optimal weight:    5.9990
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.057  14098  Z= 0.168
  Angle     :  0.426   6.137  19117  Z= 0.233
  Chirality :  0.041   0.192   2345
  Planarity :  0.003   0.047   2429
  Dihedral  :  3.828  16.222   1988
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer Outliers :  1.15 %
  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:  2.65 (0.19), residues: 1813
  helix:  3.22 (0.15), residues: 1015
  sheet:  1.09 (0.30), residues: 238
  loop : -0.84 (0.25), residues: 560

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 313
  time to evaluate  : 1.787 
Fit side-chains
  outliers start: 17
  outliers final: 7
  residues processed: 323
  average time/residue: 0.2159
  time to fit residues: 107.4516
Evaluate side-chains
  298 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 291
  time to evaluate  : 1.721 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1263
  time to fit residues: 3.9336
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 169 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 128 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 148 optimal weight:    0.9980
   chunk 98 optimal weight:    3.9990
   chunk 175 optimal weight:    5.9990
   chunk 109 optimal weight:    9.9990
   chunk 106 optimal weight:    0.7980
   chunk 80 optimal weight:    6.9990
   overall best weight:    1.2982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.051  14098  Z= 0.184
  Angle     :  0.438   5.790  19117  Z= 0.238
  Chirality :  0.041   0.188   2345
  Planarity :  0.003   0.055   2429
  Dihedral  :  3.857  19.691   1988
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer Outliers :  1.08 %
  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:  2.60 (0.19), residues: 1813
  helix:  3.15 (0.15), residues: 1015
  sheet:  1.09 (0.30), residues: 238
  loop : -0.82 (0.25), residues: 560

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 301
  time to evaluate  : 1.567 
Fit side-chains
  outliers start: 16
  outliers final: 10
  residues processed: 307
  average time/residue: 0.2102
  time to fit residues: 100.0890
Evaluate side-chains
  292 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 282
  time to evaluate  : 1.746 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.1295
  time to fit residues: 4.6522
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 70 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0970
   chunk 52 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 33 optimal weight:    0.6980
   chunk 111 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 137 optimal weight:    5.9990
   overall best weight:    1.3182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.056  14098  Z= 0.187
  Angle     :  0.441   5.881  19117  Z= 0.241
  Chirality :  0.041   0.204   2345
  Planarity :  0.003   0.042   2429
  Dihedral  :  3.862  20.115   1988
  Min Nonbonded Distance : 2.272

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer Outliers :  0.74 %
  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:  2.56 (0.19), residues: 1813
  helix:  3.10 (0.15), residues: 1015
  sheet:  0.77 (0.28), residues: 273
  loop : -0.73 (0.27), residues: 525

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 295
  time to evaluate  : 1.745 
Fit side-chains
  outliers start: 11
  outliers final: 5
  residues processed: 301
  average time/residue: 0.2281
  time to fit residues: 104.7333
Evaluate side-chains
  288 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 283
  time to evaluate  : 1.683 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1355
  time to fit residues: 3.5395
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 159 optimal weight:   10.0000
   chunk 168 optimal weight:    3.9990
   chunk 153 optimal weight:    4.9990
   chunk 163 optimal weight:    7.9990
   chunk 98 optimal weight:    0.9990
   chunk 71 optimal weight:    0.6980
   chunk 128 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 147 optimal weight:    0.9980
   chunk 154 optimal weight:    2.9990
   chunk 162 optimal weight:    0.9980
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.061  14098  Z= 0.164
  Angle     :  0.450   7.863  19117  Z= 0.243
  Chirality :  0.042   0.217   2345
  Planarity :  0.003   0.056   2429
  Dihedral  :  3.825  19.445   1988
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Rotamer Outliers :  0.20 %
  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:  2.56 (0.19), residues: 1813
  helix:  3.13 (0.15), residues: 1015
  sheet:  1.09 (0.30), residues: 238
  loop : -0.87 (0.25), residues: 560

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 298
  time to evaluate  : 1.538 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 300
  average time/residue: 0.2116
  time to fit residues: 98.5846
Evaluate side-chains
  284 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 283
  time to evaluate  : 1.578 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1211
  time to fit residues: 2.3612
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 172 optimal weight:    6.9990
   chunk 105 optimal weight:    1.9990
   chunk 82 optimal weight:    7.9990
   chunk 120 optimal weight:    5.9990
   chunk 181 optimal weight:    0.8980
   chunk 166 optimal weight:    4.9990
   chunk 144 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0870
   chunk 111 optimal weight:    1.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    1.1562

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.057  14098  Z= 0.176
  Angle     :  0.455   7.281  19117  Z= 0.244
  Chirality :  0.041   0.210   2345
  Planarity :  0.003   0.054   2429
  Dihedral  :  3.844  19.040   1988
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer Outliers :  0.54 %
  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:  2.53 (0.19), residues: 1813
  helix:  3.09 (0.15), residues: 1015
  sheet:  1.08 (0.30), residues: 238
  loop : -0.86 (0.25), residues: 560

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

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

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3626 Ramachandran restraints generated.
    1813 Oldfield, 0 Emsley, 1813 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 287
  time to evaluate  : 1.652 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 289
  average time/residue: 0.2191
  time to fit residues: 97.5044
Evaluate side-chains
  290 residues out of total 1477 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 283
  time to evaluate  : 1.640 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1461
  time to fit residues: 4.4382
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 114 optimal weight:    6.9990
   chunk 153 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 133 optimal weight:    5.9990
   chunk 21 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9980
   chunk 144 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 148 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   chunk 26 optimal weight:    7.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3472 r_free = 0.3472 target = 0.109831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.092575 restraints weight = 30312.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.094926 restraints weight = 14735.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.096586 restraints weight = 9051.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14098  Z= 0.153
  Angle     :  0.448   7.357  19117  Z= 0.240
  Chirality :  0.041   0.208   2345
  Planarity :  0.003   0.055   2429
  Dihedral  :  3.796  18.452   1988
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer Outliers :  0.20 %
  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:  2.55 (0.19), residues: 1813
  helix:  3.13 (0.15), residues: 1015
  sheet:  1.09 (0.30), residues: 238
  loop : -0.90 (0.25), residues: 560

===============================================================================
Job complete
usr+sys time: 2680.27 seconds
wall clock time: 49 minutes 27.85 seconds (2967.85 seconds total)