Starting phenix.real_space_refine
on Wed Mar  4 11:58:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6uzh_20959/03_2026/6uzh_20959.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6uzh_20959/03_2026/6uzh_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6uzh_20959/03_2026/6uzh_20959.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6uzh_20959/03_2026/6uzh_20959.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6uzh_20959/03_2026/6uzh_20959.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6uzh_20959/03_2026/6uzh_20959.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.27, per 1000 atoms: 0.24
  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: 1.05
  Conformation dependent library (CDL) restraints added in 612.9 milliseconds
  

  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: 0.55
  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: 2.47

  Time building geometry restraints manager: 1.44 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: 0.01
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:             0.920
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.010
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.810
-------------------------------------------------------------------------------
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 : 4.35
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.007   0.000   ARG G 128 
 TYR   0.010   0.002   TYR G 250 
 PHE   0.018   0.003   PHE C 277 
 TRP   0.011   0.002   TRP C 251 

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

*********************** 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  : 0.481 
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: 0.1541
  time to fit residues: 50.5362
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  : 0.419 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.4980
   chunk 149 optimal weight:    0.0470
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.129677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.093814 restraints weight = 17047.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 1.92
r_work: 0.2830 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1689

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= 0.124
  Angle     :  0.532   9.165  18641  Z= 0.285
  Chirality :  0.042   0.168   2282
  Planarity :  0.004   0.054   2366
  Dihedral  :  5.432  49.059   1941
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.17 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.58 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.85 (0.18), residues: 1764
  helix: -0.32 (0.15), residues: 973
  sheet: -1.92 (0.26), residues: 245
  loop : -2.37 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 180 
 TYR   0.004   0.001   TYR G 250 
 PHE   0.023   0.001   PHE B 277 
 TRP   0.005   0.001   TRP G 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (13748)
  covalent geometry    : angle       0.53212 (18641)
  hydrogen bonds       : bond        0.03811 (  959)
  hydrogen bonds       : angle       4.60170 ( 2814)

*********************** 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
  229 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 207
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 MET cc_start: 0.9203 (ptt) cc_final: 0.8975 (ptp)
REVERT: A  252 ASP cc_start: 0.8845 (m-30) cc_final: 0.8574 (m-30)
REVERT: B   47 MET cc_start: 0.6742 (ppp) cc_final: 0.6339 (ppp)
REVERT: B   56 MET cc_start: 0.6775 (mtm) cc_final: 0.5503 (mmt)
REVERT: B  155 MET cc_start: 0.9029 (ptt) cc_final: 0.8805 (ptt)
REVERT: C  181 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8362 (mt-10)
REVERT: C  252 ASP cc_start: 0.8947 (m-30) cc_final: 0.8722 (m-30)
REVERT: D   47 MET cc_start: 0.6991 (ppp) cc_final: 0.6547 (ppp)
REVERT: D   56 MET cc_start: 0.6262 (mtp) cc_final: 0.5827 (mmt)
REVERT: D   61 ILE cc_start: 0.5449 (OUTLIER) cc_final: 0.5215 (pt)
REVERT: D  155 MET cc_start: 0.9220 (ptt) cc_final: 0.8973 (ptp)
REVERT: E   77 ILE cc_start: 0.7788 (OUTLIER) cc_final: 0.7545 (mp)
REVERT: E  123 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8138 (tt)
REVERT: E  128 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7275 (ptp-110)
REVERT: F   82 LEU cc_start: 0.8306 (mm) cc_final: 0.8046 (tt)
REVERT: F  126 MET cc_start: 0.7874 (ptp) cc_final: 0.7412 (ptm)
REVERT: G  123 LEU cc_start: 0.8597 (tp) cc_final: 0.8240 (mp)
REVERT: G  161 LYS cc_start: 0.8942 (mtmt) cc_final: 0.8497 (mtmm)
REVERT: G  239 VAL cc_start: 0.8700 (OUTLIER) cc_final: 0.8334 (m)
  outliers start: 22
  outliers final: 8
  residues processed: 225
  average time/residue: 0.1159
  time to fit residues: 38.7134
Evaluate side-chains
  182 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 169
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 ASP
Chi-restraints excluded: chain B residue  123 LEU
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 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 84 optimal weight:    0.9990
   chunk 138 optimal weight:    0.5980
   chunk 152 optimal weight:    8.9990
   chunk 108 optimal weight:    2.9990
   chunk 151 optimal weight:    5.9990
   chunk 99 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 19 optimal weight:    0.4980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3421 r_free = 0.3421 target = 0.129857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.093417 restraints weight = 17171.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.99
r_work: 0.2822 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13748  Z= 0.122
  Angle     :  0.502  10.561  18641  Z= 0.268
  Chirality :  0.042   0.149   2282
  Planarity :  0.003   0.033   2366
  Dihedral  :  5.038  42.353   1941
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.57 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.31 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.19), residues: 1764
  helix:  0.74 (0.16), residues: 973
  sheet: -1.93 (0.25), residues: 315
  loop : -1.94 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F 224 
 TYR   0.007   0.001   TYR E 135 
 PHE   0.025   0.001   PHE B 277 
 TRP   0.004   0.001   TRP G 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (13748)
  covalent geometry    : angle       0.50156 (18641)
  hydrogen bonds       : bond        0.03566 (  959)
  hydrogen bonds       : angle       4.30285 ( 2814)

*********************** 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
  231 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 203
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7362 (mtp) cc_final: 0.7029 (ppp)
REVERT: A  155 MET cc_start: 0.9212 (ptt) cc_final: 0.9003 (ptp)
REVERT: A  159 ASP cc_start: 0.9097 (p0) cc_final: 0.8722 (p0)
REVERT: A  161 LYS cc_start: 0.8975 (mtpt) cc_final: 0.8702 (mtmm)
REVERT: A  252 ASP cc_start: 0.8875 (m-30) cc_final: 0.8555 (m-30)
REVERT: B   47 MET cc_start: 0.6743 (ppp) cc_final: 0.6307 (ppp)
REVERT: B  155 MET cc_start: 0.8994 (ptt) cc_final: 0.8778 (ptt)
REVERT: B  161 LYS cc_start: 0.8845 (mtmt) cc_final: 0.8553 (mtmm)
REVERT: B  277 PHE cc_start: 0.7600 (p90) cc_final: 0.7144 (p90)
REVERT: C   56 MET cc_start: 0.6555 (mtp) cc_final: 0.5732 (mmt)
REVERT: C  181 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8306 (mt-10)
REVERT: C  239 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8385 (m)
REVERT: C  252 ASP cc_start: 0.9072 (m-30) cc_final: 0.8786 (m-30)
REVERT: D   47 MET cc_start: 0.6999 (ppp) cc_final: 0.6504 (ppp)
REVERT: E   56 MET cc_start: 0.4728 (mmt) cc_final: 0.4490 (mmm)
REVERT: E   77 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7584 (mp)
REVERT: E  123 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8144 (tt)
REVERT: E  128 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7234 (ptp90)
REVERT: E  239 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8411 (m)
REVERT: F  270 TYR cc_start: 0.9121 (m-80) cc_final: 0.8712 (m-80)
REVERT: G   47 MET cc_start: 0.6868 (ppp) cc_final: 0.6536 (ppp)
REVERT: G  123 LEU cc_start: 0.8551 (tp) cc_final: 0.8270 (mp)
REVERT: G  161 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8788 (mtmm)
REVERT: G  227 GLU cc_start: 0.8739 (tt0) cc_final: 0.8480 (tt0)
REVERT: G  239 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8402 (m)
  outliers start: 28
  outliers final: 11
  residues processed: 220
  average time/residue: 0.1176
  time to fit residues: 38.2802
Evaluate side-chains
  194 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 177
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  126 MET
Chi-restraints excluded: chain E residue   77 ILE
Chi-restraints excluded: chain E residue   83 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 20 optimal weight:    0.9980
   chunk 131 optimal weight:    8.9990
   chunk 142 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 83 optimal weight:    5.9990
   chunk 127 optimal weight:   30.0000
   chunk 158 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    1.5984

-------------------------------------------------------------------------------
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 = 0.3381 r_free = 0.3381 target = 0.126758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.090345 restraints weight = 17224.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.2888 rms_B_bonded: 1.91
r_work: 0.2762 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2618 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13748  Z= 0.184
  Angle     :  0.537   8.565  18641  Z= 0.287
  Chirality :  0.043   0.201   2282
  Planarity :  0.003   0.032   2366
  Dihedral  :  5.019  37.426   1939
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.14 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.49 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.19), residues: 1764
  helix:  1.05 (0.16), residues: 973
  sheet: -1.81 (0.26), residues: 301
  loop : -1.89 (0.25), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G 224 
 TYR   0.005   0.001   TYR D 250 
 PHE   0.021   0.002   PHE B 277 
 TRP   0.004   0.001   TRP F 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (13748)
  covalent geometry    : angle       0.53698 (18641)
  hydrogen bonds       : bond        0.03718 (  959)
  hydrogen bonds       : angle       4.32523 ( 2814)

*********************** 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
  214 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 177
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7405 (mtp) cc_final: 0.7042 (ppp)
REVERT: A  161 LYS cc_start: 0.8910 (mtpt) cc_final: 0.8555 (mtmm)
REVERT: B   47 MET cc_start: 0.6575 (ppp) cc_final: 0.6115 (ppp)
REVERT: B   56 MET cc_start: 0.6374 (mtm) cc_final: 0.5256 (mmt)
REVERT: B  155 MET cc_start: 0.9095 (ptt) cc_final: 0.8831 (ptt)
REVERT: B  161 LYS cc_start: 0.8835 (mtmt) cc_final: 0.8502 (mtmm)
REVERT: C   56 MET cc_start: 0.6750 (mtp) cc_final: 0.5765 (mmt)
REVERT: C  123 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7938 (mp)
REVERT: C  155 MET cc_start: 0.9137 (ptp) cc_final: 0.8836 (ptm)
REVERT: C  181 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8338 (mm-30)
REVERT: D   47 MET cc_start: 0.6824 (ppp) cc_final: 0.6343 (ppp)
REVERT: D   61 ILE cc_start: 0.5557 (OUTLIER) cc_final: 0.5302 (pt)
REVERT: D  181 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8136 (mt-10)
REVERT: E   77 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7595 (mp)
REVERT: E  123 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8124 (tt)
REVERT: E  128 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7489 (ptp-110)
REVERT: E  161 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8772 (mtmm)
REVERT: F   82 LEU cc_start: 0.8107 (tt) cc_final: 0.7725 (mm)
REVERT: G   47 MET cc_start: 0.6756 (ppp) cc_final: 0.6394 (ppp)
REVERT: G  161 LYS cc_start: 0.9099 (mtmt) cc_final: 0.8716 (mtmm)
REVERT: G  227 GLU cc_start: 0.8807 (tt0) cc_final: 0.8546 (tt0)
REVERT: G  239 VAL cc_start: 0.8763 (OUTLIER) cc_final: 0.8405 (m)
  outliers start: 37
  outliers final: 22
  residues processed: 203
  average time/residue: 0.1102
  time to fit residues: 33.4928
Evaluate side-chains
  197 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
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  187 GLU
Chi-restraints excluded: chain A residue  213 ASP
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   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 D residue  128 ARG
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  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 38 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 152 optimal weight:    9.9990
   chunk 87 optimal weight:    0.7980
   chunk 118 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0470
   chunk 30 optimal weight:    5.9990
   chunk 149 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0970
   chunk 52 optimal weight:    5.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.5076

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.130848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.095427 restraints weight = 17272.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 1.91
r_work: 0.2847 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2707 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.2463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13748  Z= 0.108
  Angle     :  0.482  10.409  18641  Z= 0.260
  Chirality :  0.041   0.234   2282
  Planarity :  0.003   0.027   2366
  Dihedral  :  4.673  32.593   1939
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.57 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.64 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.19), residues: 1764
  helix:  1.45 (0.16), residues: 973
  sheet: -1.12 (0.29), residues: 266
  loop : -2.13 (0.23), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 224 
 TYR   0.005   0.000   TYR E 135 
 PHE   0.018   0.001   PHE B 277 
 TRP   0.005   0.001   TRP A 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (13748)
  covalent geometry    : angle       0.48180 (18641)
  hydrogen bonds       : bond        0.03373 (  959)
  hydrogen bonds       : angle       4.16160 ( 2814)

*********************** 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
  224 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 199
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7325 (mtp) cc_final: 0.7029 (ppp)
REVERT: A  159 ASP cc_start: 0.9022 (p0) cc_final: 0.8647 (p0)
REVERT: A  161 LYS cc_start: 0.8884 (mtpt) cc_final: 0.8648 (mtmm)
REVERT: A  217 LYS cc_start: 0.8738 (mmtp) cc_final: 0.8512 (mmtm)
REVERT: A  252 ASP cc_start: 0.8862 (m-30) cc_final: 0.8520 (m-30)
REVERT: B   47 MET cc_start: 0.6585 (ppp) cc_final: 0.6177 (ppp)
REVERT: B   56 MET cc_start: 0.6527 (mtm) cc_final: 0.5364 (mmt)
REVERT: B  155 MET cc_start: 0.8942 (ptt) cc_final: 0.8713 (ptt)
REVERT: B  161 LYS cc_start: 0.8720 (mtmt) cc_final: 0.8417 (mtmm)
REVERT: C   56 MET cc_start: 0.6517 (mtp) cc_final: 0.5531 (mmt)
REVERT: C  123 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7903 (mp)
REVERT: C  155 MET cc_start: 0.9090 (ptp) cc_final: 0.8747 (ptm)
REVERT: C  161 LYS cc_start: 0.9024 (mtpt) cc_final: 0.8823 (mtpt)
REVERT: C  181 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8240 (mt-10)
REVERT: C  239 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8288 (m)
REVERT: D   47 MET cc_start: 0.6855 (ppp) cc_final: 0.6354 (ppp)
REVERT: E   77 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7452 (mp)
REVERT: E  123 LEU cc_start: 0.8419 (tt) cc_final: 0.8079 (tt)
REVERT: E  128 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7323 (ptp-110)
REVERT: E  239 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8295 (m)
REVERT: F  270 TYR cc_start: 0.9087 (m-80) cc_final: 0.8680 (m-80)
REVERT: G   47 MET cc_start: 0.6878 (ppp) cc_final: 0.6488 (ppp)
REVERT: G   56 MET cc_start: 0.6267 (mtm) cc_final: 0.5457 (mmt)
REVERT: G  161 LYS cc_start: 0.9070 (mtmt) cc_final: 0.8684 (mtmm)
REVERT: G  227 GLU cc_start: 0.8784 (tt0) cc_final: 0.8517 (tt0)
REVERT: G  239 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8285 (m)
REVERT: G  270 TYR cc_start: 0.9057 (m-80) cc_final: 0.8753 (m-80)
  outliers start: 25
  outliers final: 7
  residues processed: 213
  average time/residue: 0.1092
  time to fit residues: 34.8970
Evaluate side-chains
  185 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 172
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain B residue  221 MET
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 E residue   77 ILE
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   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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 97 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 152 optimal weight:    8.9990
   chunk 107 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 127 optimal weight:   30.0000
   chunk 82 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 102 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
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 = 0.3373 r_free = 0.3373 target = 0.125944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.090427 restraints weight = 17215.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 1.87
r_work: 0.2764 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2620 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2343

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= 0.205
  Angle     :  0.540   8.584  18641  Z= 0.287
  Chirality :  0.043   0.238   2282
  Planarity :  0.003   0.028   2366
  Dihedral  :  4.877  30.033   1939
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.65 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.96 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.06 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.20), residues: 1764
  helix:  1.42 (0.16), residues: 966
  sheet: -1.46 (0.26), residues: 315
  loop : -1.89 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 224 
 TYR   0.005   0.001   TYR G 250 
 PHE   0.018   0.002   PHE C 277 
 TRP   0.004   0.001   TRP G 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (13748)
  covalent geometry    : angle       0.54017 (18641)
  hydrogen bonds       : bond        0.03695 (  959)
  hydrogen bonds       : angle       4.30046 ( 2814)

*********************** 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
  208 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 175
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7371 (mtp) cc_final: 0.7029 (ppp)
REVERT: A  161 LYS cc_start: 0.8920 (mtpt) cc_final: 0.8556 (mtmm)
REVERT: B   56 MET cc_start: 0.6524 (mtm) cc_final: 0.5390 (mmt)
REVERT: B  155 MET cc_start: 0.9088 (ptt) cc_final: 0.8808 (ptt)
REVERT: B  161 LYS cc_start: 0.8836 (mtmt) cc_final: 0.8509 (mtmm)
REVERT: C   56 MET cc_start: 0.6614 (mtp) cc_final: 0.5499 (mmt)
REVERT: C  123 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7950 (mp)
REVERT: C  155 MET cc_start: 0.9176 (ptp) cc_final: 0.8842 (ptm)
REVERT: C  181 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8266 (mt-10)
REVERT: D   47 MET cc_start: 0.6806 (ppp) cc_final: 0.6319 (ppp)
REVERT: D  187 GLU cc_start: 0.9274 (tt0) cc_final: 0.8873 (tt0)
REVERT: E   77 ILE cc_start: 0.7753 (OUTLIER) cc_final: 0.7483 (mp)
REVERT: E  123 LEU cc_start: 0.8462 (tt) cc_final: 0.8109 (tt)
REVERT: E  128 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7545 (ptp-110)
REVERT: E  161 LYS cc_start: 0.9083 (mtmt) cc_final: 0.8547 (mtmm)
REVERT: F   82 LEU cc_start: 0.8070 (tt) cc_final: 0.7685 (mm)
REVERT: G   47 MET cc_start: 0.6782 (ppp) cc_final: 0.6401 (ppp)
REVERT: G  161 LYS cc_start: 0.9085 (mtmt) cc_final: 0.8702 (mtmm)
REVERT: G  227 GLU cc_start: 0.8886 (tt0) cc_final: 0.8641 (tt0)
REVERT: G  239 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8382 (m)
  outliers start: 33
  outliers final: 19
  residues processed: 196
  average time/residue: 0.1063
  time to fit residues: 31.8179
Evaluate side-chains
  197 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.562 
-------------------------------------------------------------------------------
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  187 GLU
Chi-restraints excluded: chain A residue  222 THR
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  123 LEU
Chi-restraints excluded: chain D residue  125 VAL
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain D residue  136 VAL
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue   77 ILE
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  239 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 144 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 163 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 96 optimal weight:    0.7980
   chunk 127 optimal weight:   30.0000
   chunk 133 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3431 r_free = 0.3431 target = 0.130533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.095356 restraints weight = 16895.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 1.92
r_work: 0.2833 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2690 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13748  Z= 0.125
  Angle     :  0.487   8.872  18641  Z= 0.262
  Chirality :  0.042   0.247   2282
  Planarity :  0.003   0.024   2366
  Dihedral  :  4.662  29.017   1939
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.85 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 18.86 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.20), residues: 1764
  helix:  1.56 (0.16), residues: 973
  sheet: -1.02 (0.28), residues: 280
  loop : -2.19 (0.24), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 224 
 TYR   0.005   0.001   TYR E 135 
 PHE   0.017   0.001   PHE C 277 
 TRP   0.004   0.001   TRP D 240 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (13748)
  covalent geometry    : angle       0.48698 (18641)
  hydrogen bonds       : bond        0.03422 (  959)
  hydrogen bonds       : angle       4.19418 ( 2814)

*********************** 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
  209 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 184
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7363 (mtp) cc_final: 0.7078 (ppp)
REVERT: A  159 ASP cc_start: 0.9091 (p0) cc_final: 0.8754 (p0)
REVERT: A  161 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8732 (mtmm)
REVERT: A  217 LYS cc_start: 0.8727 (mmtp) cc_final: 0.8480 (mmtm)
REVERT: A  252 ASP cc_start: 0.8939 (m-30) cc_final: 0.8605 (m-30)
REVERT: B   47 MET cc_start: 0.6669 (ppp) cc_final: 0.6177 (ppp)
REVERT: B   56 MET cc_start: 0.6473 (mtm) cc_final: 0.5426 (mmt)
REVERT: B  155 MET cc_start: 0.8999 (ptt) cc_final: 0.8735 (ptt)
REVERT: B  161 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8569 (mtmm)
REVERT: C  123 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8088 (mp)
REVERT: C  239 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8395 (m)
REVERT: D   47 MET cc_start: 0.6971 (ppp) cc_final: 0.6468 (ppp)
REVERT: E   77 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7563 (mp)
REVERT: E  123 LEU cc_start: 0.8519 (tt) cc_final: 0.8241 (tt)
REVERT: E  128 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7538 (ptp-110)
REVERT: E  239 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8423 (m)
REVERT: F   82 LEU cc_start: 0.8219 (tt) cc_final: 0.7829 (mm)
REVERT: F  270 TYR cc_start: 0.9114 (m-80) cc_final: 0.8675 (m-80)
REVERT: G   47 MET cc_start: 0.6967 (ppp) cc_final: 0.6525 (ppp)
REVERT: G   56 MET cc_start: 0.6317 (mtm) cc_final: 0.5522 (mmt)
REVERT: G  161 LYS cc_start: 0.9180 (mtmt) cc_final: 0.8805 (mtmm)
REVERT: G  227 GLU cc_start: 0.8855 (tt0) cc_final: 0.8625 (tt0)
REVERT: G  239 VAL cc_start: 0.8723 (OUTLIER) cc_final: 0.8371 (m)
  outliers start: 25
  outliers final: 11
  residues processed: 201
  average time/residue: 0.1049
  time to fit residues: 31.9211
Evaluate side-chains
  183 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  187 GLU
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  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  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  239 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 129 optimal weight:   10.0000
   chunk 91 optimal weight:    3.9990
   chunk 166 optimal weight:    0.9980
   chunk 149 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 109 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 10 optimal weight:    0.1980
   chunk 96 optimal weight:    3.9990
   chunk 75 optimal weight:    7.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 200 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.132604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.098554 restraints weight = 16641.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 1.72
r_work: 0.2887 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13748  Z= 0.116
  Angle     :  0.483   8.141  18641  Z= 0.260
  Chirality :  0.042   0.249   2282
  Planarity :  0.003   0.024   2366
  Dihedral  :  4.556  29.060   1939
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.02 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 19.42 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.20), residues: 1764
  helix:  1.79 (0.17), residues: 952
  sheet: -0.93 (0.29), residues: 266
  loop : -2.10 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 224 
 TYR   0.004   0.001   TYR E 135 
 PHE   0.015   0.001   PHE C 277 
 TRP   0.003   0.001   TRP G 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (13748)
  covalent geometry    : angle       0.48347 (18641)
  hydrogen bonds       : bond        0.03373 (  959)
  hydrogen bonds       : angle       4.12266 ( 2814)

*********************** 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
  202 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 180
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7300 (mtp) cc_final: 0.7074 (ppp)
REVERT: A   88 ARG cc_start: 0.7246 (tpt170) cc_final: 0.6748 (tpp80)
REVERT: A  161 LYS cc_start: 0.8992 (mtpt) cc_final: 0.8678 (mtmm)
REVERT: A  217 LYS cc_start: 0.8746 (mmtp) cc_final: 0.8498 (mmtm)
REVERT: B   47 MET cc_start: 0.6648 (ppp) cc_final: 0.6156 (ppp)
REVERT: B   56 MET cc_start: 0.6481 (mtm) cc_final: 0.5438 (mmt)
REVERT: B  155 MET cc_start: 0.8917 (ptt) cc_final: 0.8673 (ptt)
REVERT: B  161 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8450 (mtmm)
REVERT: C   56 MET cc_start: 0.6333 (mtm) cc_final: 0.5419 (mmt)
REVERT: C  123 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7924 (mp)
REVERT: C  155 MET cc_start: 0.9129 (ptp) cc_final: 0.8751 (ptm)
REVERT: C  239 VAL cc_start: 0.8724 (OUTLIER) cc_final: 0.8309 (m)
REVERT: D   47 MET cc_start: 0.6904 (ppp) cc_final: 0.6402 (ppp)
REVERT: E   83 ILE cc_start: 0.7935 (pt) cc_final: 0.7655 (pt)
REVERT: E   91 VAL cc_start: 0.8429 (t) cc_final: 0.8140 (p)
REVERT: E  123 LEU cc_start: 0.8394 (tt) cc_final: 0.8113 (tt)
REVERT: E  128 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7540 (ptp-110)
REVERT: E  239 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8346 (m)
REVERT: F   56 MET cc_start: 0.5700 (mtp) cc_final: 0.5047 (mmt)
REVERT: F   82 LEU cc_start: 0.8157 (tt) cc_final: 0.7761 (mm)
REVERT: F  270 TYR cc_start: 0.9102 (m-80) cc_final: 0.8709 (m-80)
REVERT: G   47 MET cc_start: 0.7084 (ppp) cc_final: 0.6681 (ppp)
REVERT: G   56 MET cc_start: 0.6309 (mtm) cc_final: 0.5664 (mmt)
REVERT: G  161 LYS cc_start: 0.9068 (mtmt) cc_final: 0.8659 (mtmm)
REVERT: G  227 GLU cc_start: 0.8850 (tt0) cc_final: 0.8605 (tt0)
REVERT: G  239 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8287 (m)
  outliers start: 22
  outliers final: 11
  residues processed: 192
  average time/residue: 0.1061
  time to fit residues: 30.9099
Evaluate side-chains
  206 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 190
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  222 THR
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  126 MET
Chi-restraints excluded: chain E residue   29 VAL
Chi-restraints excluded: chain E residue  128 ARG
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  138 LEU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   96 VAL
Chi-restraints excluded: chain G residue  239 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 135 optimal weight:    0.0570
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 137 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 152 optimal weight:    3.9990
   overall best weight:    0.7498

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.132954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.098494 restraints weight = 16702.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.72
r_work: 0.2885 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2747 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13748  Z= 0.120
  Angle     :  0.488   7.922  18641  Z= 0.261
  Chirality :  0.042   0.240   2282
  Planarity :  0.003   0.032   2366
  Dihedral  :  4.522  29.178   1939
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  4.02 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 19.83 %
    Favored  : 78.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.20), residues: 1764
  helix:  1.84 (0.17), residues: 952
  sheet: -0.88 (0.30), residues: 266
  loop : -2.10 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 224 
 TYR   0.004   0.001   TYR E 135 
 PHE   0.014   0.001   PHE C 277 
 TRP   0.003   0.000   TRP G 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (13748)
  covalent geometry    : angle       0.48832 (18641)
  hydrogen bonds       : bond        0.03349 (  959)
  hydrogen bonds       : angle       4.11652 ( 2814)

*********************** 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: 22
    poor density    : 195
  time to evaluate  : 0.499 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7306 (mtp) cc_final: 0.7085 (ppp)
REVERT: A  159 ASP cc_start: 0.8948 (p0) cc_final: 0.8606 (p0)
REVERT: A  161 LYS cc_start: 0.9020 (mtpt) cc_final: 0.8713 (mtmm)
REVERT: A  217 LYS cc_start: 0.8726 (mmtp) cc_final: 0.8465 (mmtm)
REVERT: A  252 ASP cc_start: 0.8903 (m-30) cc_final: 0.8542 (m-30)
REVERT: B   47 MET cc_start: 0.6653 (ppp) cc_final: 0.6145 (ppp)
REVERT: B   56 MET cc_start: 0.6492 (mtm) cc_final: 0.5490 (mmt)
REVERT: B  155 MET cc_start: 0.8912 (ptt) cc_final: 0.8650 (ptt)
REVERT: B  161 LYS cc_start: 0.8780 (mtmt) cc_final: 0.8485 (mtmm)
REVERT: C   56 MET cc_start: 0.5966 (mtm) cc_final: 0.5133 (mmt)
REVERT: C  123 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7963 (mp)
REVERT: C  155 MET cc_start: 0.9159 (ptp) cc_final: 0.8780 (ptm)
REVERT: C  239 VAL cc_start: 0.8752 (OUTLIER) cc_final: 0.8345 (m)
REVERT: D   47 MET cc_start: 0.6913 (ppp) cc_final: 0.6420 (ppp)
REVERT: E   83 ILE cc_start: 0.7947 (pt) cc_final: 0.7658 (pt)
REVERT: E  239 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8385 (m)
REVERT: F   56 MET cc_start: 0.5520 (mtp) cc_final: 0.4873 (mmt)
REVERT: F  161 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8706 (mtmm)
REVERT: F  270 TYR cc_start: 0.9109 (m-80) cc_final: 0.8713 (m-80)
REVERT: G   47 MET cc_start: 0.7127 (ppp) cc_final: 0.6724 (ppp)
REVERT: G   56 MET cc_start: 0.6345 (mtm) cc_final: 0.5788 (mmt)
REVERT: G  161 LYS cc_start: 0.9102 (mtmt) cc_final: 0.8711 (mtmm)
REVERT: G  227 GLU cc_start: 0.8826 (tt0) cc_final: 0.8601 (tt0)
REVERT: G  239 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8316 (m)
  outliers start: 22
  outliers final: 15
  residues processed: 210
  average time/residue: 0.0977
  time to fit residues: 31.9550
Evaluate side-chains
  196 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 177
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
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  187 GLU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  227 GLU
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  123 LEU
Chi-restraints excluded: chain D residue  126 MET
Chi-restraints excluded: chain E residue   29 VAL
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  138 LEU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue   96 VAL
Chi-restraints excluded: chain G residue  239 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 142 optimal weight:    0.6980
   chunk 134 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 169 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 100 optimal weight:   10.0000
   chunk 111 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    5.9990
   chunk 150 optimal weight:    0.0670
   chunk 141 optimal weight:    2.9990
   overall best weight:    0.6518

-------------------------------------------------------------------------------
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 = 0.3471 r_free = 0.3471 target = 0.134025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.099659 restraints weight = 16610.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.71
r_work: 0.2902 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044  13748  Z= 0.114
  Angle     :  0.487   7.772  18641  Z= 0.260
  Chirality :  0.042   0.235   2282
  Planarity :  0.003   0.036   2366
  Dihedral  :  4.453  29.284   1939
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.80 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 20.04 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.20), residues: 1764
  helix:  1.91 (0.17), residues: 952
  sheet: -0.80 (0.30), residues: 266
  loop : -2.09 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 224 
 TYR   0.004   0.000   TYR E 135 
 PHE   0.014   0.001   PHE C 277 
 TRP   0.003   0.000   TRP G 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 (13748)
  covalent geometry    : angle       0.48663 (18641)
  hydrogen bonds       : bond        0.03304 (  959)
  hydrogen bonds       : angle       4.09003 ( 2814)

********************** 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
  210 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 187
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7360 (mtp) cc_final: 0.7115 (ppp)
REVERT: A  159 ASP cc_start: 0.8969 (p0) cc_final: 0.8610 (p0)
REVERT: A  161 LYS cc_start: 0.9002 (mtpt) cc_final: 0.8693 (mtmm)
REVERT: A  217 LYS cc_start: 0.8737 (mmtp) cc_final: 0.8488 (mmtm)
REVERT: B   47 MET cc_start: 0.6624 (ppp) cc_final: 0.6121 (ppp)
REVERT: B   56 MET cc_start: 0.6509 (mtm) cc_final: 0.5503 (mmt)
REVERT: B  155 MET cc_start: 0.8892 (ptt) cc_final: 0.8650 (ptt)
REVERT: B  161 LYS cc_start: 0.8717 (mtmt) cc_final: 0.8411 (mtmm)
REVERT: C   56 MET cc_start: 0.6054 (mtm) cc_final: 0.5199 (mmt)
REVERT: C  123 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7974 (mp)
REVERT: C  155 MET cc_start: 0.9069 (ptp) cc_final: 0.8691 (ptm)
REVERT: C  239 VAL cc_start: 0.8750 (OUTLIER) cc_final: 0.8356 (m)
REVERT: D   47 MET cc_start: 0.6860 (ppp) cc_final: 0.6390 (ppp)
REVERT: E  239 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8381 (m)
REVERT: F   56 MET cc_start: 0.5495 (mtp) cc_final: 0.4865 (mmt)
REVERT: F  270 TYR cc_start: 0.9121 (m-80) cc_final: 0.8741 (m-80)
REVERT: G   47 MET cc_start: 0.7098 (ppp) cc_final: 0.6690 (ppp)
REVERT: G  161 LYS cc_start: 0.9058 (mtmt) cc_final: 0.8665 (mtmm)
REVERT: G  227 GLU cc_start: 0.8780 (tt0) cc_final: 0.8546 (tt0)
REVERT: G  239 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8291 (m)
REVERT: G  245 ASP cc_start: 0.7860 (m-30) cc_final: 0.7639 (m-30)
  outliers start: 23
  outliers final: 18
  residues processed: 202
  average time/residue: 0.0971
  time to fit residues: 30.6664
Evaluate side-chains
  196 residues out of total 1442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 174
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
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  187 GLU
Chi-restraints excluded: chain A residue  222 THR
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain B residue   99 VAL
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  123 LEU
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  126 MET
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  138 LEU
Chi-restraints excluded: chain G residue   29 VAL
Chi-restraints excluded: chain G residue  239 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 161 optimal weight:    0.3980
   chunk 133 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 152 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 174 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3458 r_free = 0.3458 target = 0.132926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.098681 restraints weight = 16761.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.74
r_work: 0.2887 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13748  Z= 0.123
  Angle     :  0.502  11.146  18641  Z= 0.265
  Chirality :  0.042   0.233   2282
  Planarity :  0.003   0.036   2366
  Dihedral  :  4.469  29.298   1939
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 20.53 %
    Favored  : 77.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.20), residues: 1764
  helix:  1.92 (0.17), residues: 952
  sheet: -0.81 (0.30), residues: 266
  loop : -2.07 (0.23), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 224 
 TYR   0.004   0.001   TYR E 135 
 PHE   0.014   0.001   PHE C 277 
 TRP   0.003   0.000   TRP G 251 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (13748)
  covalent geometry    : angle       0.50245 (18641)
  hydrogen bonds       : bond        0.03348 (  959)
  hydrogen bonds       : angle       4.14291 ( 2814)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3270.90 seconds
wall clock time: 56 minutes 42.72 seconds (3402.72 seconds total)