Starting phenix.real_space_refine
on Thu Jul 31 12:06:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uzh_20959/07_2025/6uzh_20959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uzh_20959/07_2025/6uzh_20959.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uzh_20959/07_2025/6uzh_20959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uzh_20959/07_2025/6uzh_20959.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uzh_20959/07_2025/6uzh_20959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uzh_20959/07_2025/6uzh_20959.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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    8715      2.51       5
     N    2373      2.21       5
     O    2443      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13573
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "B"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "C"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "D"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "E"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "F"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
    Chain: "G"
      Number of atoms: 1939
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1939
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 5, 'TRANS': 248}
  Time building chain proxies: 7.83, per 1000 atoms: 0.58
  Number of scatterers: 13573
  At special positions: 0
  Unit cell: (98, 97, 130, 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    2443      8.00
     N    2373      7.00
     C    8715      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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.61
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3276

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 9 sheets defined
      54.4% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 60
      removed outlier: 3.562A  pdb=" N   ILE A  31 " --> pdb=" O   TYR A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 90
      removed outlier: 3.635A  pdb=" N   GLY A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 111
    Processing helix  chain 'A' and resid 111 through 127
    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 32 through 60
      removed outlier: 3.593A  pdb=" N   LEU B  42 " --> pdb=" O   ILE B  38 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE B  43 " --> pdb=" O   ILE B  39 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE B  44 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   MET B  47 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 90
      removed outlier: 3.673A  pdb=" N   GLY B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 111
    Processing helix  chain 'B' and resid 111 through 127
    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 28 through 59
      removed outlier: 3.518A  pdb=" N   SER C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 90
      removed outlier: 3.567A  pdb=" N   GLY C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 111
    Processing helix  chain 'C' and resid 111 through 127
    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 28 through 60
    Processing helix  chain 'D' and resid 63 through 90
      removed outlier: 3.505A  pdb=" N   GLY D  90 " --> pdb=" O   LEU D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 93 through 111
      removed outlier: 3.646A  pdb=" N   ILE D  97 " --> pdb=" O   THR D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 111 through 127
    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 28 through 59
    Processing helix  chain 'E' and resid 65 through 90
      removed outlier: 3.645A  pdb=" N   GLY E  90 " --> pdb=" O   LEU E  86 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 93 through 111
      removed outlier: 3.680A  pdb=" N   ALA E  98 " --> pdb=" O   ALA E  94 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 111 through 127
    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 28 through 60
    Processing helix  chain 'F' and resid 62 through 87
    Processing helix  chain 'F' and resid 94 through 127
      removed outlier: 3.531A  pdb=" N   ALA F 102 " --> pdb=" O   ALA F  98 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ALA F 110 " --> pdb=" O   ALA F 106 " (cutoff:3.500A)
      removed outlier: 4.960A  pdb=" N   ASN F 117 " --> pdb=" O   GLY F 113 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU F 118 " --> pdb=" O   SER F 114 " (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 28 through 60
    Processing helix  chain 'G' and resid 62 through 90
      removed outlier: 3.883A  pdb=" N   PHE G  68 " --> pdb=" O   THR G  64 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLY G  90 " --> pdb=" O   LEU G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 93 through 111
    Processing helix  chain 'G' and resid 111 through 127
    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 137
      removed outlier: 6.859A  pdb=" N   THR A 154 " --> pdb=" O   LEU A 146 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   VAL A 148 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   SER A 152 " --> pdb=" O   VAL A 148 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   THR G 154 " --> pdb=" O   LEU G 146 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   VAL G 148 " --> pdb=" O   SER G 152 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   SER G 152 " --> pdb=" O   VAL G 148 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   THR F 154 " --> pdb=" O   LEU F 146 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   VAL F 148 " --> pdb=" O   SER F 152 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   SER F 152 " --> pdb=" O   VAL F 148 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   THR E 154 " --> pdb=" O   LEU E 146 " (cutoff:3.500A)
      removed outlier: 5.090A  pdb=" N   VAL E 148 " --> pdb=" O   SER E 152 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   SER E 152 " --> pdb=" O   VAL E 148 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   THR D 154 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 5.106A  pdb=" N   VAL D 148 " --> pdb=" O   SER D 152 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   SER D 152 " --> pdb=" O   VAL D 148 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   THR C 154 " --> pdb=" O   LEU C 146 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   VAL C 148 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   SER C 152 " --> pdb=" O   VAL C 148 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   THR B 154 " --> pdb=" O   LEU B 146 " (cutoff:3.500A)
      removed outlier: 5.047A  pdb=" N   VAL B 148 " --> pdb=" O   SER B 152 " (cutoff:3.500A)
      removed outlier: 6.802A  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: 6.683A  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 279
      removed outlier: 7.597A  pdb=" N   MET B 273 " --> pdb=" O   GLN A 272 " (cutoff:3.500A)
      removed outlier: 5.993A  pdb=" N   ASP A 274 " --> pdb=" O   MET B 273 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   VAL B 275 " --> pdb=" O   ASP A 274 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   ASN A 276 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   PHE B 277 " --> pdb=" O   ASN A 276 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LYS A 278 " --> pdb=" O   PHE B 277 " (cutoff:3.500A)
      removed outlier: 7.562A  pdb=" N   MET C 273 " --> pdb=" O   GLN B 272 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   ASP B 274 " --> pdb=" O   MET C 273 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   VAL C 275 " --> pdb=" O   ASP B 274 " (cutoff:3.500A)
      removed outlier: 5.913A  pdb=" N   ASN B 276 " --> pdb=" O   VAL C 275 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   PHE C 277 " --> pdb=" O   ASN B 276 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   MET D 273 " --> pdb=" O   GLN C 272 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   ASP C 274 " --> pdb=" O   MET D 273 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   VAL D 275 " --> pdb=" O   ASP C 274 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   ASN C 276 " --> pdb=" O   VAL D 275 " (cutoff:3.500A)
      removed outlier: 7.332A  pdb=" N   PHE D 277 " --> pdb=" O   ASN C 276 " (cutoff:3.500A)
      removed outlier: 7.695A  pdb=" N   MET E 273 " --> pdb=" O   GLN D 272 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   ASP D 274 " --> pdb=" O   MET E 273 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   VAL E 275 " --> pdb=" O   ASP D 274 " (cutoff:3.500A)
      removed outlier: 5.911A  pdb=" N   ASN D 276 " --> pdb=" O   VAL E 275 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   PHE E 277 " --> pdb=" O   ASN D 276 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   LYS D 278 " --> pdb=" O   PHE E 277 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   MET F 273 " --> pdb=" O   GLN E 272 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   ASP E 274 " --> pdb=" O   MET F 273 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL F 275 " --> pdb=" O   ASP E 274 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   ASN E 276 " --> pdb=" O   VAL F 275 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   PHE F 277 " --> pdb=" O   ASN E 276 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   MET G 273 " --> pdb=" O   GLN F 272 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   ASP F 274 " --> pdb=" O   MET G 273 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   VAL G 275 " --> pdb=" O   ASP F 274 " (cutoff:3.500A)
      removed outlier: 6.073A  pdb=" N   ASN F 276 " --> pdb=" O   VAL G 275 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   PHE G 277 " --> pdb=" O   ASN F 276 " (cutoff:3.500A)
      removed outlier: 7.032A  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: 6.688A  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: 6.670A  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: 6.648A  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: 6.666A  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: 6.669A  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: 6.676A  pdb=" N   ASN G 234 " --> pdb=" O   ASN G 226 " (cutoff:3.500A)

    959 hydrogen bonds defined for protein.
    2814 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: 4.59

  Time building geometry restraints manager: 3.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4340
        1.34 -     1.46: 1988
        1.46 -     1.57: 7335
        1.57 -     1.69: 1
        1.69 -     1.81: 84
  Bond restraints: 13748
  Sorted by residual:
  bond pdb=" CG  LEU F 246 "
       pdb=" CD1 LEU F 246 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.39e+00
  bond pdb=" CA  VAL B  32 "
       pdb=" C   VAL B  32 "
    ideal  model  delta    sigma   weight residual
    1.523  1.546 -0.023 1.27e-02 6.20e+03 3.33e+00
  bond pdb=" CG1 ILE A 170 "
       pdb=" CD1 ILE A 170 "
    ideal  model  delta    sigma   weight residual
    1.513  1.443  0.070 3.90e-02 6.57e+02 3.18e+00
  bond pdb=" CB  VAL E 239 "
       pdb=" CG1 VAL E 239 "
    ideal  model  delta    sigma   weight residual
    1.521  1.464  0.057 3.30e-02 9.18e+02 3.01e+00
  bond pdb=" CG1 ILE E 170 "
       pdb=" CD1 ILE E 170 "
    ideal  model  delta    sigma   weight residual
    1.513  1.448  0.065 3.90e-02 6.57e+02 2.74e+00
  ... (remaining 13743 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 18075
        2.36 -     4.73: 483
        4.73 -     7.09: 67
        7.09 -     9.45: 14
        9.45 -    11.82: 2
  Bond angle restraints: 18641
  Sorted by residual:
  angle pdb=" N   VAL B  65 "
        pdb=" CA  VAL B  65 "
        pdb=" C   VAL B  65 "
      ideal   model   delta    sigma   weight residual
     113.43  106.39    7.04 1.09e+00 8.42e-01 4.17e+01
  angle pdb=" C   LYS E 278 "
        pdb=" N   ARG E 279 "
        pdb=" CA  ARG E 279 "
      ideal   model   delta    sigma   weight residual
     120.82  129.61   -8.79 1.50e+00 4.44e-01 3.44e+01
  angle pdb=" C   ILE B  31 "
        pdb=" N   VAL B  32 "
        pdb=" CA  VAL B  32 "
      ideal   model   delta    sigma   weight residual
     121.97  130.63   -8.66 1.80e+00 3.09e-01 2.31e+01
  angle pdb=" C   LYS E  60 "
        pdb=" N   ILE E  61 "
        pdb=" CA  ILE E  61 "
      ideal   model   delta    sigma   weight residual
     121.97  130.29   -8.32 1.80e+00 3.09e-01 2.14e+01
  angle pdb=" N   VAL B  32 "
        pdb=" CA  VAL B  32 "
        pdb=" C   VAL B  32 "
      ideal   model   delta    sigma   weight residual
     109.34  118.69   -9.35 2.08e+00 2.31e-01 2.02e+01
  ... (remaining 18636 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 7371
       18.00 -    36.00: 763
       36.00 -    54.00: 115
       54.00 -    72.00: 4
       72.00 -    90.00: 7
  Dihedral angle restraints: 8260
    sinusoidal: 3171
      harmonic: 5089
  Sorted by residual:
  dihedral pdb=" CA  ILE B  31 "
           pdb=" C   ILE B  31 "
           pdb=" N   VAL B  32 "
           pdb=" CA  VAL B  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -127.72  -52.28     0      5.00e+00 4.00e-02 1.09e+02
  dihedral pdb=" CA  GLY F  90 "
           pdb=" C   GLY F  90 "
           pdb=" N   VAL F  91 "
           pdb=" CA  VAL F  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.11  -39.89     0      5.00e+00 4.00e-02 6.36e+01
  dihedral pdb=" CA  LYS G  60 "
           pdb=" C   LYS G  60 "
           pdb=" N   ILE G  61 "
           pdb=" CA  ILE G  61 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -146.56  -33.44     0      5.00e+00 4.00e-02 4.47e+01
  ... (remaining 8257 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1614
       0.053 -    0.105: 491
       0.105 -    0.158: 129
       0.158 -    0.210: 36
       0.210 -    0.263: 12
  Chirality restraints: 2282
  Sorted by residual:
  chirality pdb=" CB  ILE B  31 "
            pdb=" CA  ILE B  31 "
            pdb=" CG1 ILE B  31 "
            pdb=" CG2 ILE B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  VAL C 280 "
            pdb=" CA  VAL C 280 "
            pdb=" CG1 VAL C 280 "
            pdb=" CG2 VAL C 280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CB  ILE A 233 "
            pdb=" CA  ILE A 233 "
            pdb=" CG1 ILE A 233 "
            pdb=" CG2 ILE A 233 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 2279 not shown)

  Planarity restraints: 2366
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR F 270 "   -0.042 5.00e-02 4.00e+02   6.35e-02 6.45e+00
        pdb=" N   PRO F 271 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO F 271 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO F 271 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 270 "   -0.040 5.00e-02 4.00e+02   6.02e-02 5.81e+00
        pdb=" N   PRO A 271 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR D 270 "   -0.039 5.00e-02 4.00e+02   5.92e-02 5.60e+00
        pdb=" N   PRO D 271 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO D 271 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO D 271 "   -0.033 5.00e-02 4.00e+02
  ... (remaining 2363 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3947
        2.81 -     3.34: 12389
        3.34 -     3.86: 23192
        3.86 -     4.38: 25817
        4.38 -     4.90: 46424
  Nonbonded interactions: 111769
  Sorted by model distance:
  nonbonded pdb=" OH  TYR F 194 "
            pdb=" O   GLY F 229 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   LYS D 202 "
            pdb=" OG1 THR D 206 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD1 ASP G  62 "
            pdb=" OG1 THR G  64 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" O   LYS G 202 "
            pdb=" OG1 THR G 206 "
     model   vdw
     2.311 3.040
  nonbonded pdb=" O   LYS C 202 "
            pdb=" OG1 THR C 206 "
     model   vdw
     2.313 3.040
  ... (remaining 111764 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     33.920
  Find NCS groups from input model:        0.670
  Set up NCS constraints:                  0.080
  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:3.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
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      :  0.008   0.070  13748  Z= 0.329
  Angle     :  0.954  11.816  18641  Z= 0.536
  Chirality :  0.058   0.263   2282
  Planarity :  0.006   0.064   2366
  Dihedral  : 14.158  89.995   4984
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.97 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  9.57 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

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: -3.97 (0.15), residues: 1764
  helix: -2.49 (0.12), residues: 952
  sheet: -2.71 (0.22), residues: 329
  loop : -2.18 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 251 
 PHE   0.018   0.003   PHE C 277 
 TYR   0.010   0.002   TYR G 250 
 ARG   0.007   0.000   ARG G 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11281 (  959)
  hydrogen bonds       : angle       6.19072 ( 2814)
  covalent geometry    : bond        0.00783 (13748)
  covalent geometry    : angle       0.95367 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 237
  time to evaluate  : 1.750 
Fit side-chains
REVERT: A  155 MET cc_start: 0.8792 (ptt) cc_final: 0.8507 (ptt)
REVERT: B   47 MET cc_start: 0.6880 (ppp) cc_final: 0.6376 (ppp)
REVERT: B   56 MET cc_start: 0.5808 (mtm) cc_final: 0.5227 (mmt)
REVERT: B  155 MET cc_start: 0.8672 (ptt) cc_final: 0.8465 (ptt)
REVERT: C  212 GLU cc_start: 0.8425 (tp30) cc_final: 0.8075 (tp30)
REVERT: D   47 MET cc_start: 0.7268 (ppp) cc_final: 0.7012 (ppp)
REVERT: D   61 ILE cc_start: 0.5018 (OUTLIER) cc_final: 0.4702 (pt)
REVERT: D  155 MET cc_start: 0.8855 (ptt) cc_final: 0.8553 (ptm)
REVERT: D  187 GLU cc_start: 0.8505 (tt0) cc_final: 0.8183 (tt0)
REVERT: D  202 LYS cc_start: 0.8666 (mtmt) cc_final: 0.8460 (mtpp)
REVERT: E   83 ILE cc_start: 0.8164 (pt) cc_final: 0.7948 (pt)
REVERT: G   47 MET cc_start: 0.7164 (ppp) cc_final: 0.6933 (ppp)
  outliers start: 4
  outliers final: 0
  residues processed: 241
  average time/residue: 0.3967
  time to fit residues: 129.4995
Evaluate side-chains
  164 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 2.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   61 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    0.7980
   chunk 132 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 137 optimal weight:    0.6980
   chunk 53 optimal weight:    8.9990
   chunk 83 optimal weight:    0.6980
   chunk 102 optimal weight:    5.9990
   chunk 158 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  30 ASN
A  50 ASN
A 167 ASN
B  50 ASN
B 167 ASN
C  30 ASN
C  50 ASN
C 167 ASN
D  30 ASN
D 167 ASN
E  30 ASN
E 167 ASN
F 167 ASN
G  50 ASN
G 167 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.129327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.093257 restraints weight = 16890.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 1.92
r_work: 0.2825 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2682 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  13748  Z= 0.132
  Angle     :  0.534   9.153  18641  Z= 0.286
  Chirality :  0.042   0.169   2282
  Planarity :  0.004   0.053   2366
  Dihedral  :  5.444  48.846   1941
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.23 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.58 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.85 (0.18), residues: 1764
  helix: -0.31 (0.15), residues: 973
  sheet: -1.93 (0.27), residues: 245
  loop : -2.37 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP G 251 
 PHE   0.022   0.001   PHE B 277 
 TYR   0.005   0.001   TYR G 250 
 ARG   0.006   0.000   ARG B 180 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03806 (  959)
  hydrogen bonds       : angle       4.60286 ( 2814)
  covalent geometry    : bond        0.00280 (13748)
  covalent geometry    : angle       0.53412 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 209
  time to evaluate  : 1.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 MET cc_start: 0.9219 (ptt) cc_final: 0.8993 (ptp)
REVERT: A  252 ASP cc_start: 0.8859 (m-30) cc_final: 0.8597 (m-30)
REVERT: B   47 MET cc_start: 0.6723 (ppp) cc_final: 0.6322 (ppp)
REVERT: B   56 MET cc_start: 0.6784 (mtm) cc_final: 0.5504 (mmt)
REVERT: B  155 MET cc_start: 0.9050 (ptt) cc_final: 0.8802 (ptt)
REVERT: C  181 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8353 (mt-10)
REVERT: C  252 ASP cc_start: 0.8954 (m-30) cc_final: 0.8731 (m-30)
REVERT: D   47 MET cc_start: 0.6959 (ppp) cc_final: 0.6513 (ppp)
REVERT: D   56 MET cc_start: 0.6265 (mtp) cc_final: 0.5823 (mmt)
REVERT: D   61 ILE cc_start: 0.5489 (OUTLIER) cc_final: 0.5259 (pt)
REVERT: D  155 MET cc_start: 0.9235 (ptt) cc_final: 0.8985 (ptp)
REVERT: D  187 GLU cc_start: 0.9226 (tt0) cc_final: 0.8866 (tt0)
REVERT: E   77 ILE cc_start: 0.7771 (OUTLIER) cc_final: 0.7529 (mp)
REVERT: E  123 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8152 (tt)
REVERT: E  128 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7260 (ptp-110)
REVERT: F   82 LEU cc_start: 0.8307 (mm) cc_final: 0.8038 (tt)
REVERT: F  126 MET cc_start: 0.7884 (ptp) cc_final: 0.7420 (ptm)
REVERT: G  123 LEU cc_start: 0.8604 (tp) cc_final: 0.8249 (mp)
REVERT: G  161 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8514 (mtmm)
REVERT: G  239 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8373 (m)
  outliers start: 23
  outliers final: 10
  residues processed: 228
  average time/residue: 0.2419
  time to fit residues: 81.1158
Evaluate side-chains
  190 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 175
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain E residue   77 ILE
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  128 ARG
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain G residue  125 VAL
Chi-restraints excluded: chain G residue  213 ASP
Chi-restraints excluded: chain G residue  239 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 143 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 104 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 52 optimal weight:    7.9990
   chunk 106 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 171 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 118 optimal weight:    0.8980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.127974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.091642 restraints weight = 17123.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 1.93
r_work: 0.2781 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2640 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13748  Z= 0.150
  Angle     :  0.522  10.225  18641  Z= 0.278
  Chirality :  0.042   0.149   2282
  Planarity :  0.003   0.035   2366
  Dihedral  :  5.151  43.077   1941
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.02 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 13.59 %
    Favored  : 83.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.19), residues: 1764
  helix:  0.66 (0.16), residues: 973
  sheet: -2.02 (0.25), residues: 315
  loop : -1.92 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G 251 
 PHE   0.026   0.001   PHE B 277 
 TYR   0.005   0.001   TYR E 135 
 ARG   0.004   0.000   ARG G 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03678 (  959)
  hydrogen bonds       : angle       4.37311 ( 2814)
  covalent geometry    : bond        0.00335 (13748)
  covalent geometry    : angle       0.52153 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 191
  time to evaluate  : 1.417 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7345 (mtp) cc_final: 0.7010 (ppp)
REVERT: A  155 MET cc_start: 0.9266 (ptt) cc_final: 0.9029 (ptp)
REVERT: A  159 ASP cc_start: 0.9082 (p0) cc_final: 0.8686 (p0)
REVERT: A  161 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8605 (mtmm)
REVERT: A  252 ASP cc_start: 0.8891 (m-30) cc_final: 0.8588 (m-30)
REVERT: B   47 MET cc_start: 0.6703 (ppp) cc_final: 0.6263 (ppp)
REVERT: B  155 MET cc_start: 0.9068 (ptt) cc_final: 0.8836 (ptt)
REVERT: B  161 LYS cc_start: 0.8802 (mtmt) cc_final: 0.8486 (mtmm)
REVERT: C   56 MET cc_start: 0.6692 (mtp) cc_final: 0.5796 (mmt)
REVERT: C  181 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8376 (mm-30)
REVERT: D   47 MET cc_start: 0.6952 (ppp) cc_final: 0.6462 (ppp)
REVERT: D  155 MET cc_start: 0.9302 (ptt) cc_final: 0.9059 (ptp)
REVERT: D  181 GLU cc_start: 0.8227 (mt-10) cc_final: 0.8019 (mt-10)
REVERT: D  187 GLU cc_start: 0.9264 (tt0) cc_final: 0.8908 (tt0)
REVERT: E   56 MET cc_start: 0.4475 (mmt) cc_final: 0.4254 (mmm)
REVERT: E   77 ILE cc_start: 0.7706 (OUTLIER) cc_final: 0.7452 (mp)
REVERT: E  123 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8045 (tt)
REVERT: E  128 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7354 (ptp-110)
REVERT: F   82 LEU cc_start: 0.8345 (mm) cc_final: 0.8129 (tt)
REVERT: F  246 LEU cc_start: 0.8427 (tt) cc_final: 0.8170 (tt)
REVERT: G   47 MET cc_start: 0.6785 (ppp) cc_final: 0.6460 (ppp)
REVERT: G  161 LYS cc_start: 0.8952 (mtmt) cc_final: 0.8719 (mtmm)
REVERT: G  227 GLU cc_start: 0.8791 (tt0) cc_final: 0.8539 (tt0)
REVERT: G  239 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8366 (m)
  outliers start: 35
  outliers final: 18
  residues processed: 213
  average time/residue: 0.2440
  time to fit residues: 76.8507
Evaluate side-chains
  197 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 1.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain D residue  128 ARG
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain E residue   77 ILE
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  128 ARG
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   96 VAL
Chi-restraints excluded: chain G residue  213 ASP
Chi-restraints excluded: chain G residue  239 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 92 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 70 optimal weight:    0.3980
   chunk 125 optimal weight:    0.8980
   chunk 155 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 158 optimal weight:    0.8980
   chunk 169 optimal weight:    0.7980
   chunk 130 optimal weight:    0.9980
   chunk 147 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
F 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.129512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.093534 restraints weight = 17005.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 1.90
r_work: 0.2822 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.2233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13748  Z= 0.123
  Angle     :  0.493   8.658  18641  Z= 0.267
  Chirality :  0.042   0.186   2282
  Planarity :  0.003   0.029   2366
  Dihedral  :  4.856  37.383   1939
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.51 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 15.12 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.19), residues: 1764
  helix:  1.16 (0.16), residues: 973
  sheet: -1.27 (0.28), residues: 266
  loop : -2.15 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G 251 
 PHE   0.020   0.001   PHE B 277 
 TYR   0.005   0.001   TYR E 135 
 ARG   0.003   0.000   ARG E 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  959)
  hydrogen bonds       : angle       4.23558 ( 2814)
  covalent geometry    : bond        0.00264 (13748)
  covalent geometry    : angle       0.49345 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 191
  time to evaluate  : 1.368 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7401 (mtp) cc_final: 0.7043 (ppp)
REVERT: A  155 MET cc_start: 0.9218 (ptt) cc_final: 0.8982 (ptp)
REVERT: A  159 ASP cc_start: 0.9030 (p0) cc_final: 0.8665 (p0)
REVERT: A  161 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8605 (mtmm)
REVERT: A  217 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8525 (mmtm)
REVERT: B   47 MET cc_start: 0.6570 (ppp) cc_final: 0.6128 (ppp)
REVERT: B   56 MET cc_start: 0.6568 (mtm) cc_final: 0.5434 (mmt)
REVERT: B  155 MET cc_start: 0.8999 (ptt) cc_final: 0.8773 (ptt)
REVERT: B  161 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8456 (mtmm)
REVERT: B  277 PHE cc_start: 0.7585 (p90) cc_final: 0.6890 (p90)
REVERT: C   56 MET cc_start: 0.6760 (mtp) cc_final: 0.5821 (mmt)
REVERT: C  123 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7926 (mp)
REVERT: C  161 LYS cc_start: 0.9119 (mtpt) cc_final: 0.8862 (mtmt)
REVERT: C  181 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8240 (mt-10)
REVERT: D   47 MET cc_start: 0.6847 (ppp) cc_final: 0.6360 (ppp)
REVERT: D   61 ILE cc_start: 0.5509 (OUTLIER) cc_final: 0.5237 (pt)
REVERT: D  181 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7990 (mt-10)
REVERT: D  187 GLU cc_start: 0.9212 (tt0) cc_final: 0.8831 (tt0)
REVERT: E   77 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7461 (mp)
REVERT: E  123 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8079 (tt)
REVERT: E  128 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.7245 (ptp-110)
REVERT: E  239 VAL cc_start: 0.8715 (OUTLIER) cc_final: 0.8366 (m)
REVERT: F  270 TYR cc_start: 0.9115 (m-80) cc_final: 0.8699 (m-80)
REVERT: G   47 MET cc_start: 0.6720 (ppp) cc_final: 0.6358 (ppp)
REVERT: G  161 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8727 (mtmm)
REVERT: G  227 GLU cc_start: 0.8770 (tt0) cc_final: 0.8479 (tt0)
REVERT: G  239 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8312 (m)
  outliers start: 33
  outliers final: 13
  residues processed: 215
  average time/residue: 0.2711
  time to fit residues: 84.9782
Evaluate side-chains
  191 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 171
  time to evaluate  : 1.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain D residue   61 ILE
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue   77 ILE
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  128 ARG
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain G residue   96 VAL
Chi-restraints excluded: chain G residue  213 ASP
Chi-restraints excluded: chain G residue  239 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 156 optimal weight:    1.9990
   chunk 65 optimal weight:    0.3980
   chunk 158 optimal weight:    6.9990
   chunk 110 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 141 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   chunk 165 optimal weight:    6.9990
   chunk 28 optimal weight:   30.0000
   chunk 99 optimal weight:    0.8980
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
F 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.127002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.091550 restraints weight = 17102.670|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 1.87
r_work: 0.2779 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2638 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13748  Z= 0.167
  Angle     :  0.518  10.091  18641  Z= 0.278
  Chirality :  0.043   0.241   2282
  Planarity :  0.003   0.031   2366
  Dihedral  :  4.888  33.106   1939
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.42 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.37 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.20), residues: 1764
  helix:  1.30 (0.16), residues: 973
  sheet: -1.69 (0.26), residues: 301
  loop : -1.88 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP G 251 
 PHE   0.018   0.001   PHE B 277 
 TYR   0.005   0.001   TYR G 250 
 ARG   0.008   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03616 (  959)
  hydrogen bonds       : angle       4.26960 ( 2814)
  covalent geometry    : bond        0.00379 (13748)
  covalent geometry    : angle       0.51835 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 182
  time to evaluate  : 1.411 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7383 (mtp) cc_final: 0.7039 (ppp)
REVERT: A  155 MET cc_start: 0.9254 (ptt) cc_final: 0.9014 (ptp)
REVERT: A  161 LYS cc_start: 0.8925 (mtpt) cc_final: 0.8629 (mtmm)
REVERT: B   47 MET cc_start: 0.6620 (ppp) cc_final: 0.6161 (ppp)
REVERT: B   56 MET cc_start: 0.6180 (mtm) cc_final: 0.5092 (mmt)
REVERT: B  155 MET cc_start: 0.9071 (ptt) cc_final: 0.8792 (ptt)
REVERT: B  161 LYS cc_start: 0.8828 (mtmt) cc_final: 0.8504 (mtmm)
REVERT: C   56 MET cc_start: 0.6455 (mtp) cc_final: 0.5406 (mmt)
REVERT: C  123 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7933 (mp)
REVERT: C  155 MET cc_start: 0.9179 (ptp) cc_final: 0.8804 (ptm)
REVERT: C  181 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8240 (mm-30)
REVERT: D   47 MET cc_start: 0.6843 (ppp) cc_final: 0.6350 (ppp)
REVERT: D  181 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8025 (mt-10)
REVERT: D  187 GLU cc_start: 0.9289 (tt0) cc_final: 0.8924 (tt0)
REVERT: E   77 ILE cc_start: 0.7693 (OUTLIER) cc_final: 0.7453 (mp)
REVERT: E  123 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8147 (tt)
REVERT: E  128 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7498 (ptp-110)
REVERT: F  270 TYR cc_start: 0.9126 (m-80) cc_final: 0.8693 (m-80)
REVERT: G   47 MET cc_start: 0.6818 (ppp) cc_final: 0.6448 (ppp)
REVERT: G   56 MET cc_start: 0.6276 (mtm) cc_final: 0.5467 (mmt)
REVERT: G  161 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8711 (mtmm)
REVERT: G  227 GLU cc_start: 0.8825 (tt0) cc_final: 0.8595 (tt0)
REVERT: G  239 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8374 (m)
  outliers start: 35
  outliers final: 19
  residues processed: 206
  average time/residue: 0.2215
  time to fit residues: 69.1065
Evaluate side-chains
  199 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 175
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue   77 ILE
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  128 ARG
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   96 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain G residue  213 ASP
Chi-restraints excluded: chain G residue  239 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 151 optimal weight:    6.9990
   chunk 47 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 150 optimal weight:   20.0000
   chunk 169 optimal weight:    4.9990
   chunk 170 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 10 optimal weight:    0.1980
   chunk 0 optimal weight:   20.0000
   chunk 55 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
F 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.124726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.089216 restraints weight = 17364.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.2878 rms_B_bonded: 1.88
r_work: 0.2747 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2604 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13748  Z= 0.228
  Angle     :  0.559   8.634  18641  Z= 0.297
  Chirality :  0.044   0.239   2282
  Planarity :  0.003   0.031   2366
  Dihedral  :  5.026  31.472   1939
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.82 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.31 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.20), residues: 1764
  helix:  1.24 (0.16), residues: 966
  sheet: -1.56 (0.26), residues: 315
  loop : -1.93 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP G 251 
 PHE   0.021   0.002   PHE C 277 
 TYR   0.006   0.001   TYR G 250 
 ARG   0.007   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03827 (  959)
  hydrogen bonds       : angle       4.39677 ( 2814)
  covalent geometry    : bond        0.00535 (13748)
  covalent geometry    : angle       0.55945 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 187
  time to evaluate  : 1.669 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7438 (mtp) cc_final: 0.7067 (ppp)
REVERT: A  159 ASP cc_start: 0.9096 (p0) cc_final: 0.8786 (p0)
REVERT: A  161 LYS cc_start: 0.8949 (mtpt) cc_final: 0.8646 (mtmm)
REVERT: A  252 ASP cc_start: 0.9016 (m-30) cc_final: 0.8719 (m-30)
REVERT: B   56 MET cc_start: 0.6486 (mtm) cc_final: 0.5380 (mmt)
REVERT: B  155 MET cc_start: 0.9093 (ptt) cc_final: 0.8839 (ptt)
REVERT: B  161 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8548 (mtmm)
REVERT: C  123 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7944 (mp)
REVERT: C  155 MET cc_start: 0.9222 (ptp) cc_final: 0.8850 (ptm)
REVERT: D   47 MET cc_start: 0.6895 (ppp) cc_final: 0.6408 (ppp)
REVERT: D  181 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8066 (mt-10)
REVERT: D  187 GLU cc_start: 0.9300 (tt0) cc_final: 0.8930 (tt0)
REVERT: E   77 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7492 (mp)
REVERT: E  123 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8079 (tt)
REVERT: E  128 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7587 (ptp-110)
REVERT: G   47 MET cc_start: 0.6801 (ppp) cc_final: 0.6414 (ppp)
REVERT: G  155 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8835 (ptm)
REVERT: G  161 LYS cc_start: 0.9097 (mtmt) cc_final: 0.8710 (mtmm)
REVERT: G  187 GLU cc_start: 0.9237 (tt0) cc_final: 0.9029 (tt0)
REVERT: G  227 GLU cc_start: 0.8905 (tt0) cc_final: 0.8690 (tt0)
  outliers start: 34
  outliers final: 23
  residues processed: 207
  average time/residue: 0.2352
  time to fit residues: 73.6537
Evaluate side-chains
  202 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 174
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   47 MET
Chi-restraints excluded: chain C residue   96 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   77 ILE
Chi-restraints excluded: chain D residue  123 LEU
Chi-restraints excluded: chain D residue  125 VAL
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain D residue  239 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue   77 ILE
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  126 MET
Chi-restraints excluded: chain E residue  128 ARG
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   96 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain G residue  155 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 10 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 127 optimal weight:   30.0000
   chunk 78 optimal weight:    5.9990
   chunk 15 optimal weight:    0.0870
   chunk 150 optimal weight:    0.0070
   chunk 148 optimal weight:    0.6980
   chunk 67 optimal weight:    0.8980
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
F 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.132093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2992 r_free = 0.2992 target = 0.096524 restraints weight = 17100.283|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.88
r_work: 0.2855 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2713 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  13748  Z= 0.108
  Angle     :  0.482   9.507  18641  Z= 0.260
  Chirality :  0.042   0.264   2282
  Planarity :  0.003   0.024   2366
  Dihedral  :  4.616  28.315   1939
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.68 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 19.56 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.20), residues: 1764
  helix:  1.69 (0.17), residues: 952
  sheet: -1.09 (0.29), residues: 266
  loop : -2.19 (0.22), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 240 
 PHE   0.017   0.001   PHE C 277 
 TYR   0.005   0.000   TYR E 135 
 ARG   0.006   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03357 (  959)
  hydrogen bonds       : angle       4.16654 ( 2814)
  covalent geometry    : bond        0.00221 (13748)
  covalent geometry    : angle       0.48218 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 3.004 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7327 (mtp) cc_final: 0.7071 (ppp)
REVERT: A  161 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8586 (mtmm)
REVERT: A  217 LYS cc_start: 0.8795 (mmtp) cc_final: 0.8543 (mmtm)
REVERT: B   47 MET cc_start: 0.6603 (ppp) cc_final: 0.6141 (ppp)
REVERT: B   56 MET cc_start: 0.6571 (mtm) cc_final: 0.5474 (mmt)
REVERT: B  155 MET cc_start: 0.8907 (ptt) cc_final: 0.8657 (ptt)
REVERT: B  161 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8384 (mtmm)
REVERT: B  187 GLU cc_start: 0.9147 (tt0) cc_final: 0.8893 (tt0)
REVERT: C   56 MET cc_start: 0.6241 (mtm) cc_final: 0.5299 (mmt)
REVERT: C  123 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7932 (mp)
REVERT: C  155 MET cc_start: 0.9077 (ptp) cc_final: 0.8687 (ptm)
REVERT: C  181 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8289 (mt-10)
REVERT: C  239 VAL cc_start: 0.8714 (OUTLIER) cc_final: 0.8279 (m)
REVERT: D   47 MET cc_start: 0.6828 (ppp) cc_final: 0.6347 (ppp)
REVERT: D  181 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: E   83 ILE cc_start: 0.7947 (pt) cc_final: 0.7678 (pt)
REVERT: E  123 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8033 (tt)
REVERT: E  128 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7418 (ptp-110)
REVERT: F  270 TYR cc_start: 0.9096 (m-80) cc_final: 0.8705 (m-80)
REVERT: G   47 MET cc_start: 0.7050 (ppp) cc_final: 0.6649 (ppp)
REVERT: G   56 MET cc_start: 0.6342 (mtp) cc_final: 0.5450 (mmt)
REVERT: G  161 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8732 (mtmt)
REVERT: G  227 GLU cc_start: 0.8840 (tt0) cc_final: 0.8590 (tt0)
REVERT: G  270 TYR cc_start: 0.9065 (m-80) cc_final: 0.8763 (m-80)
  outliers start: 25
  outliers final: 11
  residues processed: 210
  average time/residue: 0.2216
  time to fit residues: 70.9826
Evaluate side-chains
  195 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 180
  time to evaluate  : 1.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  128 ARG
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   96 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 102 optimal weight:    7.9990
   chunk 50 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 153 optimal weight:   10.0000
   chunk 27 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 152 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3416 r_free = 0.3416 target = 0.129334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.093292 restraints weight = 17184.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.90
r_work: 0.2823 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13748  Z= 0.143
  Angle     :  0.508   9.453  18641  Z= 0.270
  Chirality :  0.042   0.249   2282
  Planarity :  0.003   0.026   2366
  Dihedral  :  4.659  28.677   1939
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.25 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 20.11 %
    Favored  : 78.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.20), residues: 1764
  helix:  1.68 (0.17), residues: 966
  sheet: -0.81 (0.29), residues: 280
  loop : -2.09 (0.24), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP G 251 
 PHE   0.017   0.001   PHE C 277 
 TYR   0.004   0.001   TYR G 250 
 ARG   0.005   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03461 (  959)
  hydrogen bonds       : angle       4.18556 ( 2814)
  covalent geometry    : bond        0.00322 (13748)
  covalent geometry    : angle       0.50782 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 191
  time to evaluate  : 1.449 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7313 (mtp) cc_final: 0.7074 (ppp)
REVERT: A   88 ARG cc_start: 0.7222 (tpt170) cc_final: 0.6733 (tpp80)
REVERT: A  159 ASP cc_start: 0.9048 (p0) cc_final: 0.8714 (p0)
REVERT: A  161 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8598 (mtmm)
REVERT: A  217 LYS cc_start: 0.8658 (mmtp) cc_final: 0.8397 (mmtm)
REVERT: A  252 ASP cc_start: 0.8926 (m-30) cc_final: 0.8603 (m-30)
REVERT: B   47 MET cc_start: 0.6621 (ppp) cc_final: 0.6143 (ppp)
REVERT: B   56 MET cc_start: 0.6545 (mtm) cc_final: 0.5508 (mmt)
REVERT: B  155 MET cc_start: 0.9013 (ptt) cc_final: 0.8739 (ptt)
REVERT: B  161 LYS cc_start: 0.8767 (mtmt) cc_final: 0.8468 (mtmm)
REVERT: C   56 MET cc_start: 0.6001 (mtm) cc_final: 0.5147 (mmt)
REVERT: C  123 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8000 (mp)
REVERT: C  155 MET cc_start: 0.9128 (ptp) cc_final: 0.8737 (ptm)
REVERT: C  181 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: C  239 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8351 (m)
REVERT: D   47 MET cc_start: 0.6820 (ppp) cc_final: 0.6360 (ppp)
REVERT: D  181 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7927 (mt-10)
REVERT: E   91 VAL cc_start: 0.8447 (t) cc_final: 0.8157 (p)
REVERT: E  123 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8063 (tt)
REVERT: E  239 VAL cc_start: 0.8743 (OUTLIER) cc_final: 0.8384 (m)
REVERT: F   56 MET cc_start: 0.5713 (mtp) cc_final: 0.5013 (mmt)
REVERT: F  270 TYR cc_start: 0.9130 (m-80) cc_final: 0.8746 (m-80)
REVERT: G   47 MET cc_start: 0.7047 (ppp) cc_final: 0.6658 (ppp)
REVERT: G   56 MET cc_start: 0.6380 (mtp) cc_final: 0.5621 (mmt)
REVERT: G  161 LYS cc_start: 0.9067 (mtmt) cc_final: 0.8645 (mtmm)
REVERT: G  227 GLU cc_start: 0.8864 (tt0) cc_final: 0.8622 (tt0)
  outliers start: 25
  outliers final: 15
  residues processed: 207
  average time/residue: 0.2118
  time to fit residues: 67.3797
Evaluate side-chains
  198 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 179
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  221 MET
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue   97 ILE
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain E residue  239 VAL
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue   99 VAL
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   96 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 122 optimal weight:    0.6980
   chunk 139 optimal weight:    0.2980
   chunk 31 optimal weight:    5.9990
   chunk 115 optimal weight:    0.4980
   chunk 146 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0770
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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 = 0.3460 r_free = 0.3460 target = 0.133012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.097560 restraints weight = 17029.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.81
r_work: 0.2880 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  13748  Z= 0.106
  Angle     :  0.489  10.201  18641  Z= 0.260
  Chirality :  0.042   0.235   2282
  Planarity :  0.003   0.024   2366
  Dihedral  :  4.473  26.502   1939
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.29 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 20.74 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.20), residues: 1764
  helix:  1.95 (0.17), residues: 945
  sheet: -0.58 (0.29), residues: 280
  loop : -2.13 (0.23), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP F 240 
 PHE   0.014   0.001   PHE C 277 
 TYR   0.004   0.000   TYR E 135 
 ARG   0.005   0.000   ARG B 224 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  959)
  hydrogen bonds       : angle       4.10125 ( 2814)
  covalent geometry    : bond        0.00216 (13748)
  covalent geometry    : angle       0.48863 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 198
  time to evaluate  : 3.768 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7357 (mtp) cc_final: 0.7103 (ppp)
REVERT: A  159 ASP cc_start: 0.8963 (p0) cc_final: 0.8606 (p0)
REVERT: A  161 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8575 (mtmm)
REVERT: A  217 LYS cc_start: 0.8778 (mmtp) cc_final: 0.8532 (mmtm)
REVERT: B   47 MET cc_start: 0.6595 (ppp) cc_final: 0.6163 (ppp)
REVERT: B   56 MET cc_start: 0.6563 (mtm) cc_final: 0.5530 (mmt)
REVERT: B  155 MET cc_start: 0.8863 (ptt) cc_final: 0.8627 (ptt)
REVERT: B  161 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8309 (mtmm)
REVERT: C   56 MET cc_start: 0.6194 (mtm) cc_final: 0.5261 (mmt)
REVERT: C  123 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7931 (mp)
REVERT: C  155 MET cc_start: 0.9052 (ptp) cc_final: 0.8666 (ptm)
REVERT: C  181 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8323 (mt-10)
REVERT: C  239 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8247 (m)
REVERT: D   47 MET cc_start: 0.6790 (ppp) cc_final: 0.6341 (ppp)
REVERT: D  181 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: E   91 VAL cc_start: 0.8440 (t) cc_final: 0.8176 (p)
REVERT: E  123 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7998 (tt)
REVERT: F   56 MET cc_start: 0.5532 (mtp) cc_final: 0.4840 (mmt)
REVERT: F  161 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8614 (mtmm)
REVERT: F  270 TYR cc_start: 0.9103 (m-80) cc_final: 0.8730 (m-80)
REVERT: G   47 MET cc_start: 0.7086 (ppp) cc_final: 0.6700 (ppp)
REVERT: G   56 MET cc_start: 0.6460 (mtp) cc_final: 0.5789 (mmt)
REVERT: G  161 LYS cc_start: 0.8957 (mtmt) cc_final: 0.8542 (mtmm)
REVERT: G  227 GLU cc_start: 0.8758 (tt0) cc_final: 0.8506 (tt0)
REVERT: G  239 VAL cc_start: 0.8567 (t) cc_final: 0.8198 (m)
REVERT: G  270 TYR cc_start: 0.9042 (m-80) cc_final: 0.8784 (m-80)
  outliers start: 19
  outliers final: 12
  residues processed: 211
  average time/residue: 0.3599
  time to fit residues: 114.7112
Evaluate side-chains
  201 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 2.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   96 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0670
   chunk 147 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0070
   chunk 56 optimal weight:    5.9990
   chunk 125 optimal weight:   30.0000
   chunk 111 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   overall best weight:    0.7538

-------------------------------------------------------------------------------
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 = 0.3439 r_free = 0.3439 target = 0.131152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.095236 restraints weight = 17127.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 1.91
r_work: 0.2853 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.2882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13748  Z= 0.123
  Angle     :  0.503  10.815  18641  Z= 0.266
  Chirality :  0.042   0.234   2282
  Planarity :  0.003   0.055   2366
  Dihedral  :  4.500  27.550   1939
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 21.43 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.20), residues: 1764
  helix:  1.97 (0.17), residues: 945
  sheet: -0.53 (0.30), residues: 280
  loop : -2.09 (0.23), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP G 251 
 PHE   0.015   0.001   PHE C 277 
 TYR   0.004   0.001   TYR E 135 
 ARG   0.005   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03341 (  959)
  hydrogen bonds       : angle       4.12010 ( 2814)
  covalent geometry    : bond        0.00270 (13748)
  covalent geometry    : angle       0.50254 (18641)

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

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

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3528 Ramachandran restraints generated.
    1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 186
  time to evaluate  : 2.314 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7359 (mtp) cc_final: 0.7108 (ppp)
REVERT: A  161 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8619 (mtmm)
REVERT: A  217 LYS cc_start: 0.8730 (mmtp) cc_final: 0.8520 (mmtm)
REVERT: B   47 MET cc_start: 0.6596 (ppp) cc_final: 0.6107 (ppp)
REVERT: B   56 MET cc_start: 0.6565 (mtm) cc_final: 0.5528 (mmt)
REVERT: B  155 MET cc_start: 0.8937 (ptt) cc_final: 0.8701 (ptt)
REVERT: B  161 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8372 (mtmm)
REVERT: C   56 MET cc_start: 0.6120 (mtm) cc_final: 0.5273 (mmt)
REVERT: C  123 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7992 (mp)
REVERT: C  155 MET cc_start: 0.9136 (ptp) cc_final: 0.8765 (ptm)
REVERT: C  181 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8294 (mt-10)
REVERT: C  239 VAL cc_start: 0.8739 (OUTLIER) cc_final: 0.8324 (m)
REVERT: D   47 MET cc_start: 0.6775 (ppp) cc_final: 0.6328 (ppp)
REVERT: D  181 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8001 (mt-10)
REVERT: E  123 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7992 (tt)
REVERT: E  128 ARG cc_start: 0.7792 (ptt90) cc_final: 0.7507 (ptp-110)
REVERT: F   56 MET cc_start: 0.5572 (mtp) cc_final: 0.4881 (mmt)
REVERT: F  161 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8684 (mtmm)
REVERT: F  270 TYR cc_start: 0.9116 (m-80) cc_final: 0.8726 (m-80)
REVERT: G   47 MET cc_start: 0.7068 (ppp) cc_final: 0.6671 (ppp)
REVERT: G  161 LYS cc_start: 0.8990 (mtmt) cc_final: 0.8594 (mtmm)
REVERT: G  227 GLU cc_start: 0.8791 (tt0) cc_final: 0.8544 (tt0)
  outliers start: 19
  outliers final: 14
  residues processed: 199
  average time/residue: 0.3034
  time to fit residues: 94.2291
Evaluate side-chains
  199 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 2.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue  123 LEU
Chi-restraints excluded: chain C residue  221 MET
Chi-restraints excluded: chain C residue  239 VAL
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  123 LEU
Chi-restraints excluded: chain F residue   61 ILE
Chi-restraints excluded: chain F residue   91 VAL
Chi-restraints excluded: chain F residue   97 ILE
Chi-restraints excluded: chain F residue  138 LEU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   96 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 74 optimal weight:    0.0770
   chunk 161 optimal weight:    0.7980
   chunk 163 optimal weight:    0.7980
   chunk 137 optimal weight:    0.9990
   chunk 157 optimal weight:    6.9990
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    0.0470
   chunk 40 optimal weight:    1.9990
   chunk 125 optimal weight:   30.0000
   chunk 39 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5436

-------------------------------------------------------------------------------
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 = 0.3479 r_free = 0.3479 target = 0.134590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.100483 restraints weight = 16882.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 1.77
r_work: 0.2914 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  13748  Z= 0.110
  Angle     :  0.502  11.900  18641  Z= 0.264
  Chirality :  0.042   0.227   2282
  Planarity :  0.003   0.049   2366
  Dihedral  :  4.422  26.021   1939
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 21.15 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.20), residues: 1764
  helix:  2.02 (0.17), residues: 945
  sheet: -0.45 (0.30), residues: 280
  loop : -2.10 (0.23), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D 240 
 PHE   0.014   0.001   PHE C 277 
 TYR   0.004   0.000   TYR E 135 
 ARG   0.005   0.000   ARG E 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03290 (  959)
  hydrogen bonds       : angle       4.09406 ( 2814)
  covalent geometry    : bond        0.00233 (13748)
  covalent geometry    : angle       0.50234 (18641)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8090.64 seconds
wall clock time: 146 minutes 29.37 seconds (8789.37 seconds total)