Starting phenix.real_space_refine
on Tue May 20 06:36:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vxh_43617/05_2025/8vxh_43617.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vxh_43617/05_2025/8vxh_43617.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vxh_43617/05_2025/8vxh_43617.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vxh_43617/05_2025/8vxh_43617.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vxh_43617/05_2025/8vxh_43617.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vxh_43617/05_2025/8vxh_43617.cif"
  }
  resolution = 2.79
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    6212      2.51       5
     N    1692      2.21       5
     O    1756      1.98       5
     H    9956      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 19668
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4917
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 4917
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 13, 'TRANS': 298}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 11.09, per 1000 atoms: 0.56
  Number of scatterers: 19668
  At special positions: 0
  Unit cell: (112.35, 112.35, 107.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      52     16.00
     O    1756      8.00
     N    1692      7.00
     C    6212      6.00
     H    9956      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.14
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2336

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 4 sheets defined
      56.7% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 36
    Processing helix  chain 'A' and resid 53 through 64
    Processing helix  chain 'A' and resid 79 through 89
    Processing helix  chain 'A' and resid 106 through 108
      No H-bonds generated for 'chain 'A' and resid 106 through 108'
    Processing helix  chain 'A' and resid 109 through 118
    Processing helix  chain 'A' and resid 134 through 153
    Processing helix  chain 'A' and resid 168 through 175
    Processing helix  chain 'A' and resid 183 through 192
      removed outlier: 3.677A  pdb=" N   PHE A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 229
    Processing helix  chain 'A' and resid 230 through 262
      removed outlier: 3.715A  pdb=" N   ARG A 234 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU A 236 " --> pdb=" O   PRO A 232 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   SER A 237 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU A 238 " --> pdb=" O   ARG A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 304
      removed outlier: 3.710A  pdb=" N   TYR A 294 " --> pdb=" O   LEU A 290 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG A 297 " --> pdb=" O   GLU A 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 36
    Processing helix  chain 'B' and resid 53 through 64
    Processing helix  chain 'B' and resid 79 through 89
    Processing helix  chain 'B' and resid 106 through 108
      No H-bonds generated for 'chain 'B' and resid 106 through 108'
    Processing helix  chain 'B' and resid 109 through 118
    Processing helix  chain 'B' and resid 134 through 153
    Processing helix  chain 'B' and resid 168 through 175
    Processing helix  chain 'B' and resid 183 through 192
      removed outlier: 3.677A  pdb=" N   PHE B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 229
    Processing helix  chain 'B' and resid 230 through 262
      removed outlier: 3.715A  pdb=" N   ARG B 234 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU B 236 " --> pdb=" O   PRO B 232 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   SER B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU B 238 " --> pdb=" O   ARG B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 304
      removed outlier: 3.711A  pdb=" N   TYR B 294 " --> pdb=" O   LEU B 290 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG B 297 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 36
    Processing helix  chain 'C' and resid 53 through 64
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 106 through 108
      No H-bonds generated for 'chain 'C' and resid 106 through 108'
    Processing helix  chain 'C' and resid 109 through 118
    Processing helix  chain 'C' and resid 134 through 153
    Processing helix  chain 'C' and resid 168 through 175
    Processing helix  chain 'C' and resid 183 through 192
      removed outlier: 3.677A  pdb=" N   PHE C 191 " --> pdb=" O   LEU C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 229
    Processing helix  chain 'C' and resid 230 through 262
      removed outlier: 3.714A  pdb=" N   ARG C 234 " --> pdb=" O   THR C 230 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU C 236 " --> pdb=" O   PRO C 232 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   SER C 237 " --> pdb=" O   LEU C 233 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU C 238 " --> pdb=" O   ARG C 234 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 304
      removed outlier: 3.710A  pdb=" N   TYR C 294 " --> pdb=" O   LEU C 290 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG C 297 " --> pdb=" O   GLU C 293 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 22 through 36
    Processing helix  chain 'D' and resid 53 through 64
    Processing helix  chain 'D' and resid 79 through 89
    Processing helix  chain 'D' and resid 106 through 108
      No H-bonds generated for 'chain 'D' and resid 106 through 108'
    Processing helix  chain 'D' and resid 109 through 118
    Processing helix  chain 'D' and resid 134 through 153
    Processing helix  chain 'D' and resid 168 through 175
    Processing helix  chain 'D' and resid 183 through 192
      removed outlier: 3.677A  pdb=" N   PHE D 191 " --> pdb=" O   LEU D 187 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 213 through 229
    Processing helix  chain 'D' and resid 230 through 262
      removed outlier: 3.715A  pdb=" N   ARG D 234 " --> pdb=" O   THR D 230 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU D 236 " --> pdb=" O   PRO D 232 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   SER D 237 " --> pdb=" O   LEU D 233 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU D 238 " --> pdb=" O   ARG D 234 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 267 through 304
      removed outlier: 3.710A  pdb=" N   TYR D 294 " --> pdb=" O   LEU D 290 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ARG D 297 " --> pdb=" O   GLU D 293 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 200
      removed outlier: 6.403A  pdb=" N   VAL A 123 " --> pdb=" O   THR A 196 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   ILE A 198 " --> pdb=" O   VAL A 123 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLY A 125 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   VAL A 200 " --> pdb=" O   GLY A 125 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   VAL A 127 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG A 164 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   ILE A  70 " --> pdb=" O   TRP A  41 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ILE A  43 " --> pdb=" O   ILE A  70 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   ILE A  72 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   LEU A  45 " --> pdb=" O   ILE A  72 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   LEU A  74 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ASP A  47 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   SER A  71 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   VAL B 313 " --> pdb=" O   SER A  71 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   LEU A  73 " --> pdb=" O   GLN B 311 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 314
      removed outlier: 6.976A  pdb=" N   LEU D  73 " --> pdb=" O   GLN A 311 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   VAL A 313 " --> pdb=" O   SER D  71 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   SER D  71 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
      removed outlier: 8.451A  pdb=" N   ILE D  70 " --> pdb=" O   TRP D  41 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ILE D  43 " --> pdb=" O   ILE D  70 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   ILE D  72 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   LEU D  45 " --> pdb=" O   ILE D  72 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   LEU D  74 " --> pdb=" O   LEU D  45 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ASP D  47 " --> pdb=" O   LEU D  74 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG D 164 " --> pdb=" O   THR D  98 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   VAL D 123 " --> pdb=" O   THR D 196 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   ILE D 198 " --> pdb=" O   VAL D 123 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   GLY D 125 " --> pdb=" O   ILE D 198 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   VAL D 200 " --> pdb=" O   GLY D 125 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   VAL D 127 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 195 through 200
      removed outlier: 6.404A  pdb=" N   VAL B 123 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
      removed outlier: 8.107A  pdb=" N   ILE B 198 " --> pdb=" O   VAL B 123 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLY B 125 " --> pdb=" O   ILE B 198 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   VAL B 200 " --> pdb=" O   GLY B 125 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   VAL B 127 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG B 164 " --> pdb=" O   THR B  98 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   ILE B  70 " --> pdb=" O   TRP B  41 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ILE B  43 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   ILE B  72 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   LEU B  45 " --> pdb=" O   ILE B  72 " (cutoff:3.500A)
      removed outlier: 7.536A  pdb=" N   LEU B  74 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ASP B  47 " --> pdb=" O   LEU B  74 " (cutoff:3.500A)
      removed outlier: 6.833A  pdb=" N   SER B  71 " --> pdb=" O   VAL C 313 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   VAL C 313 " --> pdb=" O   SER B  71 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   LEU B  73 " --> pdb=" O   GLN C 311 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 195 through 200
      removed outlier: 6.403A  pdb=" N   VAL C 123 " --> pdb=" O   THR C 196 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   ILE C 198 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   GLY C 125 " --> pdb=" O   ILE C 198 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   VAL C 200 " --> pdb=" O   GLY C 125 " (cutoff:3.500A)
      removed outlier: 5.819A  pdb=" N   VAL C 127 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ARG C 164 " --> pdb=" O   THR C  98 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   ILE C  70 " --> pdb=" O   TRP C  41 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   ILE C  43 " --> pdb=" O   ILE C  70 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   ILE C  72 " --> pdb=" O   ILE C  43 " (cutoff:3.500A)
      removed outlier: 6.283A  pdb=" N   LEU C  45 " --> pdb=" O   ILE C  72 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   LEU C  74 " --> pdb=" O   LEU C  45 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ASP C  47 " --> pdb=" O   LEU C  74 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   SER C  71 " --> pdb=" O   VAL D 313 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   VAL D 313 " --> pdb=" O   SER C  71 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   LEU C  73 " --> pdb=" O   GLN D 311 " (cutoff:3.500A)

    576 hydrogen bonds defined for protein.
    1716 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: 7.25

  Time building geometry restraints manager: 6.12 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9940
        1.03 -     1.23: 16
        1.23 -     1.42: 4008
        1.42 -     1.61: 5788
        1.61 -     1.81: 88
  Bond restraints: 19840
  Sorted by residual:
  bond pdb=" CA  ILE A 184 "
       pdb=" CB  ILE A 184 "
    ideal  model  delta    sigma   weight residual
    1.539  1.535  0.004 5.40e-03 3.43e+04 6.76e-01
  bond pdb=" CA  ILE B 184 "
       pdb=" CB  ILE B 184 "
    ideal  model  delta    sigma   weight residual
    1.539  1.535  0.004 5.40e-03 3.43e+04 6.64e-01
  bond pdb=" CA  ILE C 184 "
       pdb=" CB  ILE C 184 "
    ideal  model  delta    sigma   weight residual
    1.539  1.535  0.004 5.40e-03 3.43e+04 6.42e-01
  bond pdb=" CA  ILE D 184 "
       pdb=" CB  ILE D 184 "
    ideal  model  delta    sigma   weight residual
    1.539  1.535  0.004 5.40e-03 3.43e+04 5.05e-01
  bond pdb=" CA  ASP B  48 "
       pdb=" C   ASP B  48 "
    ideal  model  delta    sigma   weight residual
    1.530  1.523  0.007 1.14e-02 7.69e+03 4.02e-01
  ... (remaining 19835 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.87: 32305
        0.87 -     1.74: 3398
        1.74 -     2.61: 149
        2.61 -     3.49: 48
        3.49 -     4.36: 20
  Bond angle restraints: 35920
  Sorted by residual:
  angle pdb=" C   GLU A 109 "
        pdb=" N   ILE A 110 "
        pdb=" CA  ILE A 110 "
      ideal   model   delta    sigma   weight residual
     120.33  122.74   -2.41 8.00e-01 1.56e+00 9.06e+00
  angle pdb=" C   GLU B 109 "
        pdb=" N   ILE B 110 "
        pdb=" CA  ILE B 110 "
      ideal   model   delta    sigma   weight residual
     120.33  122.73   -2.40 8.00e-01 1.56e+00 8.97e+00
  angle pdb=" C   GLU C 109 "
        pdb=" N   ILE C 110 "
        pdb=" CA  ILE C 110 "
      ideal   model   delta    sigma   weight residual
     120.33  122.72   -2.39 8.00e-01 1.56e+00 8.91e+00
  angle pdb=" C   GLU D 109 "
        pdb=" N   ILE D 110 "
        pdb=" CA  ILE D 110 "
      ideal   model   delta    sigma   weight residual
     120.33  122.71   -2.38 8.00e-01 1.56e+00 8.87e+00
  angle pdb=" C   ILE A 110 "
        pdb=" CA  ILE A 110 "
        pdb=" CB  ILE A 110 "
      ideal   model   delta    sigma   weight residual
     114.00  110.87    3.13 1.31e+00 5.83e-01 5.71e+00
  ... (remaining 35915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.13: 8657
       16.13 -    32.26: 347
       32.26 -    48.40: 151
       48.40 -    64.53: 101
       64.53 -    80.66: 8
  Dihedral angle restraints: 9264
    sinusoidal: 5128
      harmonic: 4136
  Sorted by residual:
  dihedral pdb=" CA  ARG A 303 "
           pdb=" C   ARG A 303 "
           pdb=" N   ALA A 304 "
           pdb=" CA  ALA A 304 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.19   20.81     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  ARG B 303 "
           pdb=" C   ARG B 303 "
           pdb=" N   ALA B 304 "
           pdb=" CA  ALA B 304 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.19   20.81     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  ARG D 303 "
           pdb=" C   ARG D 303 "
           pdb=" N   ALA D 304 "
           pdb=" CA  ALA D 304 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.20   20.80     0      5.00e+00 4.00e-02 1.73e+01
  ... (remaining 9261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 982
       0.025 -    0.051: 322
       0.051 -    0.076: 156
       0.076 -    0.102: 42
       0.102 -    0.127: 78
  Chirality restraints: 1580
  Sorted by residual:
  chirality pdb=" CA  ILE B  70 "
            pdb=" N   ILE B  70 "
            pdb=" C   ILE B  70 "
            pdb=" CB  ILE B  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.03e-01
  chirality pdb=" CA  ILE D  70 "
            pdb=" N   ILE D  70 "
            pdb=" C   ILE D  70 "
            pdb=" CB  ILE D  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.99e-01
  chirality pdb=" CA  ILE C  70 "
            pdb=" N   ILE C  70 "
            pdb=" C   ILE C  70 "
            pdb=" CB  ILE C  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.97e-01
  ... (remaining 1577 not shown)

  Planarity restraints: 2892
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 106 "   -0.018 5.00e-02 4.00e+02   2.65e-02 1.12e+00
        pdb=" N   PRO A 107 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 107 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 107 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 106 "    0.017 5.00e-02 4.00e+02   2.64e-02 1.11e+00
        pdb=" N   PRO B 107 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO B 107 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 107 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO D 106 "   -0.017 5.00e-02 4.00e+02   2.64e-02 1.11e+00
        pdb=" N   PRO D 107 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO D 107 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO D 107 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 2889 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 1319
        2.22 -     2.81: 41355
        2.81 -     3.41: 51167
        3.41 -     4.00: 68161
        4.00 -     4.60: 106876
  Nonbonded interactions: 268878
  Sorted by model distance:
  nonbonded pdb=" O   MET A 215 "
            pdb="HD21 ASN A 219 "
     model   vdw
     1.622 2.450
  nonbonded pdb=" O   MET D 215 "
            pdb="HD21 ASN D 219 "
     model   vdw
     1.622 2.450
  nonbonded pdb=" O   MET C 215 "
            pdb="HD21 ASN C 219 "
     model   vdw
     1.622 2.450
  nonbonded pdb=" O   MET B 215 "
            pdb="HD21 ASN B 219 "
     model   vdw
     1.623 2.450
  nonbonded pdb=" OD1 ASP B 223 "
            pdb="HH21 ARG C 297 "
     model   vdw
     1.649 2.450
  ... (remaining 268873 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.180
  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:             0.320
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.160
  Set scattering table:                    0.190
  Process input model:                     43.650
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
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      :  0.002   0.018   9884  Z= 0.109
  Angle     :  0.462   4.356  13392  Z= 0.270
  Chirality :  0.040   0.127   1580
  Planarity :  0.003   0.026   1704
  Dihedral  :  9.660  80.662   3660
  Min Nonbonded Distance : 2.365

Molprobity Statistics.
  All-atom Clashscore : 1.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.14 (0.25), residues: 1232
  helix:  3.42 (0.21), residues: 676
  sheet:  2.12 (0.39), residues: 204
  loop : -0.85 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP D  41 
 HIS   0.002   0.001   HIS A 202 
 PHE   0.006   0.001   PHE D 183 
 TYR   0.007   0.001   TYR A 299 
 ARG   0.002   0.000   ARG B 297 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13551 (  576)
  hydrogen bonds       : angle       6.03222 ( 1716)
  covalent geometry    : bond        0.00213 ( 9884)
  covalent geometry    : angle       0.46179 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  220 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 1.565 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 GLU cc_start: 0.6687 (tt0) cc_final: 0.6423 (mt-10)
REVERT: A  122 ASP cc_start: 0.8922 (m-30) cc_final: 0.8702 (m-30)
REVERT: A  149 GLN cc_start: 0.7414 (tt0) cc_final: 0.7090 (tp40)
REVERT: A  221 MET cc_start: 0.7337 (mmp) cc_final: 0.6497 (tmt)
REVERT: A  255 ILE cc_start: 0.8140 (mm) cc_final: 0.7892 (mp)
REVERT: B   64 GLU cc_start: 0.6638 (tt0) cc_final: 0.6379 (mt-10)
REVERT: B  149 GLN cc_start: 0.7354 (tt0) cc_final: 0.7092 (tp40)
REVERT: B  221 MET cc_start: 0.7292 (mmp) cc_final: 0.6413 (tmt)
REVERT: C  122 ASP cc_start: 0.8944 (m-30) cc_final: 0.8651 (m-30)
REVERT: C  149 GLN cc_start: 0.7353 (tt0) cc_final: 0.7047 (tp40)
REVERT: C  221 MET cc_start: 0.7312 (mmp) cc_final: 0.6462 (tmt)
REVERT: D   64 GLU cc_start: 0.6609 (tt0) cc_final: 0.6362 (mt-10)
REVERT: D  122 ASP cc_start: 0.8924 (m-30) cc_final: 0.8638 (m-30)
REVERT: D  149 GLN cc_start: 0.7386 (tt0) cc_final: 0.7084 (tp40)
REVERT: D  221 MET cc_start: 0.7364 (mmp) cc_final: 0.6504 (tmt)
REVERT: D  255 ILE cc_start: 0.8104 (mm) cc_final: 0.7903 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 2.1806
  time to fit residues: 520.7275
Evaluate side-chains
  162 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 112 optimal weight:    0.7980
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 130 ASN
A 132 GLN
B 130 ASN
B 132 GLN
C 130 ASN
C 132 GLN
D 130 ASN
D 132 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.151133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.116308 restraints weight = 31340.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.91
r_work: 0.3279 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   9884  Z= 0.163
  Angle     :  0.512   4.607  13392  Z= 0.276
  Chirality :  0.044   0.153   1580
  Planarity :  0.005   0.031   1704
  Dihedral  :  3.833  24.755   1368
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 1.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  5.82 %
    Favored  : 93.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.24), residues: 1232
  helix:  2.81 (0.20), residues: 692
  sheet:  2.35 (0.40), residues: 168
  loop : -1.19 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  41 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.009   0.001   PHE C 309 
 TYR   0.007   0.002   TYR C 166 
 ARG   0.003   0.001   ARG A 176 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06347 (  576)
  hydrogen bonds       : angle       4.78453 ( 1716)
  covalent geometry    : bond        0.00372 ( 9884)
  covalent geometry    : angle       0.51248 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  171 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 160
  time to evaluate  : 1.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    8 LYS cc_start: 0.8259 (ptmt) cc_final: 0.7450 (pttt)
REVERT: A   64 GLU cc_start: 0.6939 (tt0) cc_final: 0.6481 (mt-10)
REVERT: A  122 ASP cc_start: 0.9097 (m-30) cc_final: 0.8805 (m-30)
REVERT: A  149 GLN cc_start: 0.7280 (tt0) cc_final: 0.6815 (tp40)
REVERT: A  221 MET cc_start: 0.7469 (mmp) cc_final: 0.6471 (tmt)
REVERT: A  251 SER cc_start: 0.8456 (OUTLIER) cc_final: 0.8246 (m)
REVERT: B    8 LYS cc_start: 0.8150 (ptmt) cc_final: 0.7371 (pttt)
REVERT: B   64 GLU cc_start: 0.6925 (tt0) cc_final: 0.6475 (mt-10)
REVERT: B  149 GLN cc_start: 0.7137 (tt0) cc_final: 0.6702 (tp40)
REVERT: B  221 MET cc_start: 0.7601 (mmp) cc_final: 0.6637 (tmt)
REVERT: B  251 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.8013 (m)
REVERT: C    8 LYS cc_start: 0.8207 (ptmt) cc_final: 0.7431 (pttt)
REVERT: C  142 LYS cc_start: 0.7374 (mptm) cc_final: 0.7147 (mptm)
REVERT: C  149 GLN cc_start: 0.7245 (tt0) cc_final: 0.6769 (tp40)
REVERT: C  215 MET cc_start: 0.6057 (mmp) cc_final: 0.5764 (mmt)
REVERT: C  221 MET cc_start: 0.7515 (mmp) cc_final: 0.6534 (tmt)
REVERT: C  251 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7999 (m)
REVERT: D    8 LYS cc_start: 0.8174 (ptmt) cc_final: 0.7396 (pttt)
REVERT: D   64 GLU cc_start: 0.6913 (tt0) cc_final: 0.6467 (mt-10)
REVERT: D  122 ASP cc_start: 0.9113 (m-30) cc_final: 0.8842 (m-30)
REVERT: D  149 GLN cc_start: 0.7229 (tt0) cc_final: 0.6794 (tp40)
REVERT: D  221 MET cc_start: 0.7483 (mmp) cc_final: 0.6503 (tmt)
REVERT: D  251 SER cc_start: 0.8269 (OUTLIER) cc_final: 0.8017 (m)
  outliers start: 11
  outliers final: 4
  residues processed: 161
  average time/residue: 2.0299
  time to fit residues: 358.0810
Evaluate side-chains
  169 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 161
  time to evaluate  : 1.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  251 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 115 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 132 GLN
A 300 ASN
B 132 GLN
B 300 ASN
C 132 GLN
C 300 ASN
D 132 GLN
D 300 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.148807 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.113785 restraints weight = 31159.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.91
r_work: 0.3250 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3147 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   9884  Z= 0.158
  Angle     :  0.510   4.392  13392  Z= 0.272
  Chirality :  0.043   0.144   1580
  Planarity :  0.005   0.035   1704
  Dihedral  :  4.003  25.570   1368
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 1.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.35 %
    Favored  : 91.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.25), residues: 1232
  helix:  2.63 (0.20), residues: 680
  sheet:  2.15 (0.41), residues: 168
  loop : -1.44 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  41 
 HIS   0.002   0.001   HIS B  68 
 PHE   0.007   0.001   PHE C 309 
 TYR   0.006   0.001   TYR C 315 
 ARG   0.003   0.000   ARG C 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06440 (  576)
  hydrogen bonds       : angle       4.46882 ( 1716)
  covalent geometry    : bond        0.00367 ( 9884)
  covalent geometry    : angle       0.51049 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  182 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 170
  time to evaluate  : 1.449 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7518 (pttt)
REVERT: A   64 GLU cc_start: 0.7133 (tt0) cc_final: 0.6600 (mt-10)
REVERT: A  122 ASP cc_start: 0.9109 (m-30) cc_final: 0.8816 (m-30)
REVERT: A  144 ILE cc_start: 0.7459 (mm) cc_final: 0.7216 (mt)
REVERT: A  149 GLN cc_start: 0.7354 (tt0) cc_final: 0.6801 (tp40)
REVERT: A  221 MET cc_start: 0.7433 (mmp) cc_final: 0.6502 (tmm)
REVERT: A  251 SER cc_start: 0.8320 (OUTLIER) cc_final: 0.7508 (p)
REVERT: B    8 LYS cc_start: 0.8294 (ptmt) cc_final: 0.7501 (pttt)
REVERT: B   64 GLU cc_start: 0.7102 (tt0) cc_final: 0.6609 (mt-10)
REVERT: B  142 LYS cc_start: 0.7412 (mptm) cc_final: 0.7094 (mptm)
REVERT: B  149 GLN cc_start: 0.7218 (tt0) cc_final: 0.6678 (tp40)
REVERT: B  251 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7654 (p)
REVERT: B  272 MET cc_start: 0.6919 (ttp) cc_final: 0.6445 (mmm)
REVERT: C    8 LYS cc_start: 0.8329 (ptmt) cc_final: 0.7519 (pttt)
REVERT: C  144 ILE cc_start: 0.7566 (mm) cc_final: 0.7322 (mt)
REVERT: C  149 GLN cc_start: 0.7386 (tt0) cc_final: 0.6827 (tp40)
REVERT: C  215 MET cc_start: 0.6176 (mmp) cc_final: 0.5788 (mmt)
REVERT: C  251 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7648 (p)
REVERT: C  272 MET cc_start: 0.6898 (ttp) cc_final: 0.6413 (mmm)
REVERT: D    8 LYS cc_start: 0.8305 (ptmt) cc_final: 0.7495 (pttt)
REVERT: D   64 GLU cc_start: 0.7106 (tt0) cc_final: 0.6607 (mt-10)
REVERT: D  122 ASP cc_start: 0.9123 (m-30) cc_final: 0.8837 (m-30)
REVERT: D  132 GLN cc_start: 0.6749 (mt0) cc_final: 0.6472 (pp30)
REVERT: D  144 ILE cc_start: 0.7545 (mm) cc_final: 0.7313 (mt)
REVERT: D  149 GLN cc_start: 0.7191 (tt0) cc_final: 0.6653 (tp40)
REVERT: D  251 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7464 (p)
  outliers start: 12
  outliers final: 4
  residues processed: 174
  average time/residue: 1.9341
  time to fit residues: 368.8053
Evaluate side-chains
  166 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 158
  time to evaluate  : 1.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  251 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 121 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 300 ASN
B 132 GLN
B 300 ASN
C 132 GLN
C 300 ASN
D 300 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.146963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.111953 restraints weight = 31434.076|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 1.92
r_work: 0.3224 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9884  Z= 0.178
  Angle     :  0.530   5.164  13392  Z= 0.283
  Chirality :  0.043   0.144   1580
  Planarity :  0.005   0.037   1704
  Dihedral  :  4.107  26.048   1368
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.92 %
    Favored  : 90.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.24), residues: 1232
  helix:  2.38 (0.20), residues: 680
  sheet:  1.52 (0.40), residues: 176
  loop : -1.63 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  41 
 HIS   0.003   0.001   HIS C  68 
 PHE   0.008   0.001   PHE D 191 
 TYR   0.008   0.002   TYR C 315 
 ARG   0.003   0.000   ARG A 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06767 (  576)
  hydrogen bonds       : angle       4.42348 ( 1716)
  covalent geometry    : bond        0.00422 ( 9884)
  covalent geometry    : angle       0.52953 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  181 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 169
  time to evaluate  : 1.714 
Fit side-chains
   revert: symmetry clash
REVERT: A    8 LYS cc_start: 0.8340 (ptmt) cc_final: 0.7569 (pttt)
REVERT: A   60 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7840 (ttpp)
REVERT: A   64 GLU cc_start: 0.7296 (tt0) cc_final: 0.6641 (mt-10)
REVERT: A  144 ILE cc_start: 0.7461 (mm) cc_final: 0.7201 (mt)
REVERT: A  149 GLN cc_start: 0.7351 (tt0) cc_final: 0.6788 (tp40)
REVERT: A  221 MET cc_start: 0.7430 (mmp) cc_final: 0.6423 (tmm)
REVERT: A  251 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.7857 (p)
REVERT: A  265 TRP cc_start: 0.6000 (m-90) cc_final: 0.5748 (m-90)
REVERT: A  272 MET cc_start: 0.7074 (ttm) cc_final: 0.6750 (mmm)
REVERT: B    8 LYS cc_start: 0.8303 (ptmt) cc_final: 0.7518 (pttt)
REVERT: B   60 LYS cc_start: 0.8260 (ttmt) cc_final: 0.7859 (ttpp)
REVERT: B   64 GLU cc_start: 0.7268 (tt0) cc_final: 0.6640 (mt-10)
REVERT: B  132 GLN cc_start: 0.6902 (mt0) cc_final: 0.6552 (pp30)
REVERT: B  149 GLN cc_start: 0.7083 (tt0) cc_final: 0.6590 (tp40)
REVERT: B  251 SER cc_start: 0.8259 (OUTLIER) cc_final: 0.7650 (p)
REVERT: B  272 MET cc_start: 0.7120 (ttp) cc_final: 0.6702 (mmm)
REVERT: C    8 LYS cc_start: 0.8324 (ptmt) cc_final: 0.7536 (pttt)
REVERT: C  144 ILE cc_start: 0.7560 (mm) cc_final: 0.7311 (mt)
REVERT: C  149 GLN cc_start: 0.7176 (tt0) cc_final: 0.6634 (tp40)
REVERT: C  215 MET cc_start: 0.6243 (mmp) cc_final: 0.5830 (mmt)
REVERT: C  251 SER cc_start: 0.8321 (OUTLIER) cc_final: 0.7712 (p)
REVERT: C  272 MET cc_start: 0.7095 (ttp) cc_final: 0.6630 (mmm)
REVERT: D    8 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7530 (pttt)
REVERT: D   64 GLU cc_start: 0.7329 (tt0) cc_final: 0.6760 (mt-10)
REVERT: D  132 GLN cc_start: 0.6721 (mt0) cc_final: 0.6473 (pp30)
REVERT: D  144 ILE cc_start: 0.7456 (mm) cc_final: 0.7207 (mt)
REVERT: D  149 GLN cc_start: 0.7103 (tt0) cc_final: 0.6592 (tp40)
REVERT: D  251 SER cc_start: 0.8288 (OUTLIER) cc_final: 0.7494 (p)
  outliers start: 12
  outliers final: 4
  residues processed: 173
  average time/residue: 2.0460
  time to fit residues: 387.3194
Evaluate side-chains
  166 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 158
  time to evaluate  : 1.562 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  251 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 82 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 300 ASN
B 300 ASN
C 300 ASN
D 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.147426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.112661 restraints weight = 31572.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.91
r_work: 0.3228 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9884  Z= 0.160
  Angle     :  0.513   4.996  13392  Z= 0.273
  Chirality :  0.043   0.142   1580
  Planarity :  0.005   0.038   1704
  Dihedral  :  4.090  26.307   1368
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 1.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  9.16 %
    Favored  : 89.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.25), residues: 1232
  helix:  2.39 (0.20), residues: 680
  sheet:  1.44 (0.40), residues: 176
  loop : -1.73 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  41 
 HIS   0.002   0.001   HIS A  90 
 PHE   0.007   0.001   PHE C 309 
 TYR   0.007   0.001   TYR C 315 
 ARG   0.002   0.000   ARG B 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06504 (  576)
  hydrogen bonds       : angle       4.35545 ( 1716)
  covalent geometry    : bond        0.00374 ( 9884)
  covalent geometry    : angle       0.51262 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  180 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 166
  time to evaluate  : 1.659 
Fit side-chains
REVERT: A    8 LYS cc_start: 0.8330 (ptmt) cc_final: 0.7573 (pttt)
REVERT: A   64 GLU cc_start: 0.7414 (tt0) cc_final: 0.6728 (mt-10)
REVERT: A  144 ILE cc_start: 0.7450 (mm) cc_final: 0.7202 (mt)
REVERT: A  149 GLN cc_start: 0.7143 (tt0) cc_final: 0.6617 (tp40)
REVERT: A  251 SER cc_start: 0.8445 (OUTLIER) cc_final: 0.7858 (p)
REVERT: A  265 TRP cc_start: 0.6039 (m-90) cc_final: 0.5800 (m-90)
REVERT: A  272 MET cc_start: 0.7050 (ttm) cc_final: 0.6758 (mmm)
REVERT: B    8 LYS cc_start: 0.8309 (ptmt) cc_final: 0.7549 (pttt)
REVERT: B   64 GLU cc_start: 0.7391 (tt0) cc_final: 0.6712 (mt-10)
REVERT: B  118 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7889 (m-30)
REVERT: B  132 GLN cc_start: 0.6861 (mt0) cc_final: 0.6576 (pp30)
REVERT: B  142 LYS cc_start: 0.7436 (mptm) cc_final: 0.7119 (mptm)
REVERT: B  144 ILE cc_start: 0.7455 (mm) cc_final: 0.7211 (mt)
REVERT: B  149 GLN cc_start: 0.7116 (tt0) cc_final: 0.6613 (tp40)
REVERT: B  251 SER cc_start: 0.8248 (OUTLIER) cc_final: 0.7631 (p)
REVERT: B  272 MET cc_start: 0.7123 (ttp) cc_final: 0.6699 (mmm)
REVERT: C    8 LYS cc_start: 0.8301 (ptmt) cc_final: 0.7546 (pttt)
REVERT: C   60 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7897 (ttpp)
REVERT: C  132 GLN cc_start: 0.6904 (mt0) cc_final: 0.6535 (pp30)
REVERT: C  144 ILE cc_start: 0.7479 (mm) cc_final: 0.7228 (mt)
REVERT: C  149 GLN cc_start: 0.7164 (tt0) cc_final: 0.6594 (tp40)
REVERT: C  251 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.7720 (p)
REVERT: C  272 MET cc_start: 0.7101 (ttp) cc_final: 0.6638 (mmm)
REVERT: D    8 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7548 (pttt)
REVERT: D   60 LYS cc_start: 0.8273 (ttmt) cc_final: 0.7871 (ttpp)
REVERT: D   64 GLU cc_start: 0.7430 (tt0) cc_final: 0.6782 (mt-10)
REVERT: D  132 GLN cc_start: 0.6789 (mt0) cc_final: 0.6488 (pp30)
REVERT: D  144 ILE cc_start: 0.7473 (mm) cc_final: 0.7221 (mt)
REVERT: D  149 GLN cc_start: 0.7099 (tt0) cc_final: 0.6597 (tp40)
REVERT: D  251 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.7778 (p)
REVERT: D  265 TRP cc_start: 0.5963 (m-90) cc_final: 0.5646 (m-90)
  outliers start: 14
  outliers final: 4
  residues processed: 171
  average time/residue: 2.0879
  time to fit residues: 389.1770
Evaluate side-chains
  172 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 1.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  251 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 121 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 13 optimal weight:    7.9990
   chunk 111 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A 300 ASN
B 300 ASN
C 300 ASN
D 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.147196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.112546 restraints weight = 31467.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 1.91
r_work: 0.3228 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   9884  Z= 0.159
  Angle     :  0.509   4.342  13392  Z= 0.271
  Chirality :  0.042   0.143   1580
  Planarity :  0.005   0.040   1704
  Dihedral  :  4.089  26.333   1368
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 2.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  :  9.16 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.25), residues: 1232
  helix:  2.38 (0.20), residues: 680
  sheet:  1.30 (0.40), residues: 176
  loop : -1.78 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  41 
 HIS   0.002   0.001   HIS C  90 
 PHE   0.007   0.001   PHE C 309 
 TYR   0.006   0.001   TYR C 315 
 ARG   0.002   0.000   ARG B 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06472 (  576)
  hydrogen bonds       : angle       4.33355 ( 1716)
  covalent geometry    : bond        0.00372 ( 9884)
  covalent geometry    : angle       0.50860 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  183 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 1.590 
Fit side-chains
REVERT: A    8 LYS cc_start: 0.8340 (ptmt) cc_final: 0.7596 (pttt)
REVERT: A   64 GLU cc_start: 0.7488 (tt0) cc_final: 0.6871 (mt-10)
REVERT: A  144 ILE cc_start: 0.7486 (mm) cc_final: 0.7222 (mt)
REVERT: A  149 GLN cc_start: 0.7163 (tt0) cc_final: 0.6644 (tp40)
REVERT: A  221 MET cc_start: 0.7532 (mmp) cc_final: 0.6565 (tmm)
REVERT: A  251 SER cc_start: 0.8484 (OUTLIER) cc_final: 0.7909 (p)
REVERT: A  265 TRP cc_start: 0.6071 (m-90) cc_final: 0.5839 (m-90)
REVERT: A  272 MET cc_start: 0.7207 (ttm) cc_final: 0.6963 (mmm)
REVERT: B    8 LYS cc_start: 0.8314 (ptmt) cc_final: 0.7587 (pttt)
REVERT: B   64 GLU cc_start: 0.7414 (tt0) cc_final: 0.6774 (mt-10)
REVERT: B  132 GLN cc_start: 0.6900 (mt0) cc_final: 0.6567 (pp30)
REVERT: B  142 LYS cc_start: 0.7484 (mptm) cc_final: 0.7167 (mptm)
REVERT: B  144 ILE cc_start: 0.7513 (mm) cc_final: 0.7264 (mt)
REVERT: B  149 GLN cc_start: 0.7119 (tt0) cc_final: 0.6628 (tp40)
REVERT: B  251 SER cc_start: 0.8338 (OUTLIER) cc_final: 0.7734 (p)
REVERT: B  272 MET cc_start: 0.7199 (ttp) cc_final: 0.6806 (mmm)
REVERT: C    8 LYS cc_start: 0.8321 (ptmt) cc_final: 0.7596 (pttt)
REVERT: C   60 LYS cc_start: 0.8236 (ttmt) cc_final: 0.7935 (ttpp)
REVERT: C  132 GLN cc_start: 0.6966 (mt0) cc_final: 0.6557 (pp30)
REVERT: C  144 ILE cc_start: 0.7512 (mm) cc_final: 0.7254 (mt)
REVERT: C  149 GLN cc_start: 0.7166 (tt0) cc_final: 0.6689 (tp40)
REVERT: C  251 SER cc_start: 0.8359 (OUTLIER) cc_final: 0.7765 (p)
REVERT: C  272 MET cc_start: 0.7164 (ttp) cc_final: 0.6740 (mmm)
REVERT: D    8 LYS cc_start: 0.8315 (ptmt) cc_final: 0.7589 (pttt)
REVERT: D   64 GLU cc_start: 0.7470 (tt0) cc_final: 0.6780 (mt-10)
REVERT: D  132 GLN cc_start: 0.6837 (mt0) cc_final: 0.6518 (pp30)
REVERT: D  144 ILE cc_start: 0.7493 (mm) cc_final: 0.7236 (mt)
REVERT: D  149 GLN cc_start: 0.7135 (tt0) cc_final: 0.6642 (tp40)
  outliers start: 20
  outliers final: 5
  residues processed: 171
  average time/residue: 2.1058
  time to fit residues: 393.9550
Evaluate side-chains
  170 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 162
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  251 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 111 optimal weight:    0.3980
   chunk 92 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0770
   chunk 13 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 108 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 103 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.0142

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

Flipped N/Q/H residues before XYZ refinement:
A 300 ASN
B 300 ASN
C 300 ASN
D 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.148517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.113714 restraints weight = 31354.149|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.92
r_work: 0.3250 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3148 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.2933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9884  Z= 0.123
  Angle     :  0.476   4.360  13392  Z= 0.251
  Chirality :  0.041   0.141   1580
  Planarity :  0.005   0.038   1704
  Dihedral  :  3.954  25.870   1368
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  9.92 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.25), residues: 1232
  helix:  2.61 (0.20), residues: 680
  sheet:  1.34 (0.40), residues: 176
  loop : -1.79 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP D  41 
 HIS   0.003   0.001   HIS D  90 
 PHE   0.007   0.001   PHE C 309 
 TYR   0.007   0.001   TYR B 159 
 ARG   0.001   0.000   ARG C  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05712 (  576)
  hydrogen bonds       : angle       4.26226 ( 1716)
  covalent geometry    : bond        0.00270 ( 9884)
  covalent geometry    : angle       0.47638 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  180 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 170
  time to evaluate  : 1.575 
Fit side-chains
REVERT: A    8 LYS cc_start: 0.8269 (ptmt) cc_final: 0.7540 (pttt)
REVERT: A   64 GLU cc_start: 0.7428 (tt0) cc_final: 0.6787 (mt-10)
REVERT: A  144 ILE cc_start: 0.7424 (mm) cc_final: 0.7177 (mt)
REVERT: A  149 GLN cc_start: 0.7115 (tt0) cc_final: 0.6595 (tp40)
REVERT: A  251 SER cc_start: 0.8422 (OUTLIER) cc_final: 0.7833 (p)
REVERT: A  265 TRP cc_start: 0.6075 (m-90) cc_final: 0.5857 (m-90)
REVERT: B    8 LYS cc_start: 0.8278 (ptmt) cc_final: 0.7552 (pttt)
REVERT: B   60 LYS cc_start: 0.8090 (ttpt) cc_final: 0.7578 (ttpp)
REVERT: B   64 GLU cc_start: 0.7390 (tt0) cc_final: 0.6747 (mt-10)
REVERT: B  118 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7800 (m-30)
REVERT: B  132 GLN cc_start: 0.6890 (mt0) cc_final: 0.6559 (pp30)
REVERT: B  144 ILE cc_start: 0.7537 (mm) cc_final: 0.7295 (mt)
REVERT: B  149 GLN cc_start: 0.7106 (tt0) cc_final: 0.6614 (tp40)
REVERT: B  251 SER cc_start: 0.8284 (OUTLIER) cc_final: 0.7690 (p)
REVERT: B  272 MET cc_start: 0.7021 (ttp) cc_final: 0.6619 (mmm)
REVERT: C    8 LYS cc_start: 0.8246 (ptmt) cc_final: 0.7534 (pttt)
REVERT: C   60 LYS cc_start: 0.8188 (ttmt) cc_final: 0.7859 (ttpp)
REVERT: C  132 GLN cc_start: 0.6996 (mt0) cc_final: 0.6488 (pp30)
REVERT: C  144 ILE cc_start: 0.7563 (mm) cc_final: 0.7314 (mt)
REVERT: C  149 GLN cc_start: 0.7167 (tt0) cc_final: 0.6589 (tp40)
REVERT: C  251 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7682 (p)
REVERT: C  272 MET cc_start: 0.6987 (ttp) cc_final: 0.6546 (mmm)
REVERT: D    8 LYS cc_start: 0.8258 (ptmt) cc_final: 0.7545 (pttt)
REVERT: D   60 LYS cc_start: 0.8101 (ttpt) cc_final: 0.7599 (ttpp)
REVERT: D   64 GLU cc_start: 0.7438 (tt0) cc_final: 0.6786 (mt-10)
REVERT: D  132 GLN cc_start: 0.6840 (mt0) cc_final: 0.6557 (pp30)
REVERT: D  144 ILE cc_start: 0.7441 (mm) cc_final: 0.7191 (mt)
REVERT: D  149 GLN cc_start: 0.7140 (tt0) cc_final: 0.6630 (tp40)
  outliers start: 10
  outliers final: 5
  residues processed: 175
  average time/residue: 2.0450
  time to fit residues: 391.0822
Evaluate side-chains
  176 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 167
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  251 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 82 optimal weight:    0.0370
   chunk 83 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 25 optimal weight:    0.0010
   chunk 43 optimal weight:    0.0870
   chunk 27 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.6244

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

Flipped N/Q/H residues before XYZ refinement:
A 300 ASN
B 300 ASN
C 300 ASN
D 300 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.115298 restraints weight = 31395.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.92
r_work: 0.3269 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9884  Z= 0.106
  Angle     :  0.452   5.154  13392  Z= 0.238
  Chirality :  0.041   0.141   1580
  Planarity :  0.004   0.038   1704
  Dihedral  :  3.817  25.468   1368
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 1.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.11 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.99 (0.25), residues: 1232
  helix:  2.82 (0.21), residues: 680
  sheet:  1.48 (0.41), residues: 168
  loop : -1.71 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP D  41 
 HIS   0.002   0.001   HIS A  90 
 PHE   0.008   0.001   PHE C 309 
 TYR   0.006   0.001   TYR D 159 
 ARG   0.001   0.000   ARG D 303 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05081 (  576)
  hydrogen bonds       : angle       4.18161 ( 1716)
  covalent geometry    : bond        0.00219 ( 9884)
  covalent geometry    : angle       0.45188 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  182 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 173
  time to evaluate  : 1.504 
Fit side-chains
REVERT: A    8 LYS cc_start: 0.8232 (ptmt) cc_final: 0.7515 (pttt)
REVERT: A   60 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7537 (ttpp)
REVERT: A   64 GLU cc_start: 0.7407 (tt0) cc_final: 0.6730 (mt-10)
REVERT: A  144 ILE cc_start: 0.7535 (mm) cc_final: 0.7293 (mt)
REVERT: A  149 GLN cc_start: 0.7124 (tt0) cc_final: 0.6619 (tp40)
REVERT: B    8 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7517 (pttt)
REVERT: B   60 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7622 (ttpp)
REVERT: B   64 GLU cc_start: 0.7388 (tt0) cc_final: 0.6740 (mt-10)
REVERT: B  132 GLN cc_start: 0.6873 (mt0) cc_final: 0.6545 (pp30)
REVERT: B  142 LYS cc_start: 0.7399 (mptm) cc_final: 0.7058 (mptm)
REVERT: B  144 ILE cc_start: 0.7549 (mm) cc_final: 0.7304 (mt)
REVERT: B  149 GLN cc_start: 0.7143 (tt0) cc_final: 0.6568 (tp40)
REVERT: B  251 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7580 (p)
REVERT: B  272 MET cc_start: 0.6904 (ttp) cc_final: 0.6508 (mmm)
REVERT: C    8 LYS cc_start: 0.8281 (ptmt) cc_final: 0.7519 (pttt)
REVERT: C   60 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7818 (ttpp)
REVERT: C  132 GLN cc_start: 0.6946 (mt0) cc_final: 0.6538 (pp30)
REVERT: C  142 LYS cc_start: 0.7407 (mptm) cc_final: 0.7074 (mptm)
REVERT: C  144 ILE cc_start: 0.7563 (mm) cc_final: 0.7312 (mt)
REVERT: C  149 GLN cc_start: 0.7149 (tt0) cc_final: 0.6664 (tp40)
REVERT: C  251 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.7649 (p)
REVERT: C  272 MET cc_start: 0.6893 (ttp) cc_final: 0.6434 (mmm)
REVERT: D    8 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7530 (pttt)
REVERT: D   60 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7605 (ttpp)
REVERT: D   64 GLU cc_start: 0.7421 (tt0) cc_final: 0.6769 (mt-10)
REVERT: D  132 GLN cc_start: 0.6840 (mt0) cc_final: 0.6551 (pp30)
REVERT: D  144 ILE cc_start: 0.7547 (mm) cc_final: 0.7302 (mt)
REVERT: D  149 GLN cc_start: 0.7129 (tt0) cc_final: 0.6632 (tp40)
  outliers start: 9
  outliers final: 6
  residues processed: 177
  average time/residue: 2.0227
  time to fit residues: 391.2776
Evaluate side-chains
  176 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 168
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  251 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 82 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 104 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.146627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.111989 restraints weight = 31335.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.90
r_work: 0.3225 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9884  Z= 0.187
  Angle     :  0.534   5.661  13392  Z= 0.284
  Chirality :  0.043   0.146   1580
  Planarity :  0.005   0.039   1704
  Dihedral  :  4.099  26.629   1368
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 10.11 %
    Favored  : 88.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.25), residues: 1232
  helix:  2.43 (0.20), residues: 680
  sheet:  1.21 (0.40), residues: 176
  loop : -1.82 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  41 
 HIS   0.004   0.001   HIS B  81 
 PHE   0.007   0.001   PHE C 309 
 TYR   0.008   0.002   TYR D 315 
 ARG   0.002   0.000   ARG C 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06672 (  576)
  hydrogen bonds       : angle       4.25457 ( 1716)
  covalent geometry    : bond        0.00451 ( 9884)
  covalent geometry    : angle       0.53352 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  181 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 164
  time to evaluate  : 1.668 
Fit side-chains
REVERT: A    8 LYS cc_start: 0.8318 (ptmt) cc_final: 0.7566 (pttt)
REVERT: A   60 LYS cc_start: 0.8096 (ttpt) cc_final: 0.7586 (ttpp)
REVERT: A   64 GLU cc_start: 0.7526 (tt0) cc_final: 0.6861 (mt-10)
REVERT: A  144 ILE cc_start: 0.7467 (mm) cc_final: 0.7194 (mt)
REVERT: A  149 GLN cc_start: 0.7155 (tt0) cc_final: 0.6639 (tp40)
REVERT: A  221 MET cc_start: 0.7537 (mmp) cc_final: 0.6597 (tmm)
REVERT: B    8 LYS cc_start: 0.8312 (ptmt) cc_final: 0.7576 (pttt)
REVERT: B   60 LYS cc_start: 0.8163 (ttpt) cc_final: 0.7665 (ttpp)
REVERT: B   64 GLU cc_start: 0.7496 (tt0) cc_final: 0.6831 (mt-10)
REVERT: B  132 GLN cc_start: 0.6911 (mt0) cc_final: 0.6576 (pp30)
REVERT: B  142 LYS cc_start: 0.7459 (mptm) cc_final: 0.7140 (mptm)
REVERT: B  144 ILE cc_start: 0.7476 (mm) cc_final: 0.7222 (mt)
REVERT: B  149 GLN cc_start: 0.7107 (tt0) cc_final: 0.6597 (tp40)
REVERT: B  250 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7663 (mm)
REVERT: B  251 SER cc_start: 0.8243 (OUTLIER) cc_final: 0.7704 (p)
REVERT: B  272 MET cc_start: 0.7136 (ttp) cc_final: 0.6751 (mmm)
REVERT: C    8 LYS cc_start: 0.8292 (ptmt) cc_final: 0.7566 (pttt)
REVERT: C   60 LYS cc_start: 0.8198 (ttmt) cc_final: 0.7861 (ttpp)
REVERT: C  132 GLN cc_start: 0.7066 (mt0) cc_final: 0.6484 (pp30)
REVERT: C  142 LYS cc_start: 0.7495 (mptm) cc_final: 0.7165 (mptm)
REVERT: C  144 ILE cc_start: 0.7484 (mm) cc_final: 0.7230 (mt)
REVERT: C  149 GLN cc_start: 0.7181 (tt0) cc_final: 0.6612 (tp40)
REVERT: C  250 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7673 (mm)
REVERT: C  251 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7702 (p)
REVERT: C  272 MET cc_start: 0.7129 (ttp) cc_final: 0.6679 (mmm)
REVERT: D    8 LYS cc_start: 0.8313 (ptmt) cc_final: 0.7585 (pttt)
REVERT: D   60 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7656 (ttpp)
REVERT: D   64 GLU cc_start: 0.7505 (tt0) cc_final: 0.6848 (mt-10)
REVERT: D  132 GLN cc_start: 0.6958 (mt0) cc_final: 0.6532 (pp30)
REVERT: D  144 ILE cc_start: 0.7443 (mm) cc_final: 0.7193 (mt)
REVERT: D  149 GLN cc_start: 0.7137 (tt0) cc_final: 0.6628 (tp40)
  outliers start: 17
  outliers final: 6
  residues processed: 170
  average time/residue: 2.0890
  time to fit residues: 387.4348
Evaluate side-chains
  175 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 165
  time to evaluate  : 1.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  251 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 72 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 92 optimal weight:    3.9990
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3722 r_free = 0.3722 target = 0.147813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.113515 restraints weight = 31152.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.89
r_work: 0.3240 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 3.39 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9884  Z= 0.145
  Angle     :  0.498   4.831  13392  Z= 0.264
  Chirality :  0.042   0.145   1580
  Planarity :  0.005   0.038   1704
  Dihedral  :  4.029  26.219   1368
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.50 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.25), residues: 1232
  helix:  2.53 (0.20), residues: 680
  sheet:  1.12 (0.40), residues: 176
  loop : -1.82 (0.30), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C  41 
 HIS   0.003   0.001   HIS A  90 
 PHE   0.007   0.001   PHE C 309 
 TYR   0.006   0.001   TYR B 159 
 ARG   0.002   0.000   ARG D 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06081 (  576)
  hydrogen bonds       : angle       4.22017 ( 1716)
  covalent geometry    : bond        0.00332 ( 9884)
  covalent geometry    : angle       0.49765 (13392)

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

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

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2464 Ramachandran restraints generated.
    1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Residue TYR  212 is missing expected H atoms. Skipping.
Evaluate side-chains
  179 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 1.471 
Fit side-chains
REVERT: A    8 LYS cc_start: 0.8304 (ptmt) cc_final: 0.7552 (pttt)
REVERT: A   60 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7604 (ttpp)
REVERT: A   64 GLU cc_start: 0.7508 (tt0) cc_final: 0.6855 (mt-10)
REVERT: A  144 ILE cc_start: 0.7464 (mm) cc_final: 0.7208 (mt)
REVERT: A  149 GLN cc_start: 0.7116 (tt0) cc_final: 0.6589 (tp40)
REVERT: A  215 MET cc_start: 0.6081 (mmp) cc_final: 0.5751 (mmt)
REVERT: B    8 LYS cc_start: 0.8283 (ptmt) cc_final: 0.7564 (pttt)
REVERT: B   60 LYS cc_start: 0.8159 (ttpt) cc_final: 0.7663 (ttpp)
REVERT: B   64 GLU cc_start: 0.7483 (tt0) cc_final: 0.6828 (mt-10)
REVERT: B  132 GLN cc_start: 0.7005 (mt0) cc_final: 0.6525 (pp30)
REVERT: B  142 LYS cc_start: 0.7445 (mptm) cc_final: 0.7114 (mptm)
REVERT: B  144 ILE cc_start: 0.7469 (mm) cc_final: 0.7223 (mt)
REVERT: B  149 GLN cc_start: 0.7043 (tt0) cc_final: 0.6515 (tp40)
REVERT: B  250 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7641 (mm)
REVERT: B  251 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7588 (p)
REVERT: B  272 MET cc_start: 0.7076 (ttp) cc_final: 0.6696 (mmm)
REVERT: C    8 LYS cc_start: 0.8279 (ptmt) cc_final: 0.7563 (pttt)
REVERT: C   60 LYS cc_start: 0.8148 (ttmt) cc_final: 0.7842 (ttpp)
REVERT: C  132 GLN cc_start: 0.7063 (mt0) cc_final: 0.6551 (pp30)
REVERT: C  142 LYS cc_start: 0.7443 (mptm) cc_final: 0.7102 (mptm)
REVERT: C  144 ILE cc_start: 0.7481 (mm) cc_final: 0.7232 (mt)
REVERT: C  149 GLN cc_start: 0.7162 (tt0) cc_final: 0.6604 (tp40)
REVERT: C  250 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7651 (mm)
REVERT: C  251 SER cc_start: 0.8204 (OUTLIER) cc_final: 0.7598 (p)
REVERT: C  272 MET cc_start: 0.7065 (ttp) cc_final: 0.6605 (mmm)
REVERT: D    8 LYS cc_start: 0.8285 (ptmt) cc_final: 0.7562 (pttt)
REVERT: D   60 LYS cc_start: 0.8145 (ttpt) cc_final: 0.7646 (ttpp)
REVERT: D   64 GLU cc_start: 0.7468 (tt0) cc_final: 0.6805 (mt-10)
REVERT: D  132 GLN cc_start: 0.6981 (mt0) cc_final: 0.6563 (pp30)
REVERT: D  144 ILE cc_start: 0.7455 (mm) cc_final: 0.7207 (mt)
REVERT: D  149 GLN cc_start: 0.7137 (tt0) cc_final: 0.6620 (tp40)
  outliers start: 14
  outliers final: 7
  residues processed: 171
  average time/residue: 2.0671
  time to fit residues: 386.2715
Evaluate side-chains
  175 residues out of total 1060 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 164
  time to evaluate  : 1.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  100 ASP
Chi-restraints excluded: chain A residue  245 ILE
Chi-restraints excluded: chain A residue  251 SER
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain C residue  100 ASP
Chi-restraints excluded: chain C residue  250 LEU
Chi-restraints excluded: chain C residue  251 SER
Chi-restraints excluded: chain D residue  100 ASP
Chi-restraints excluded: chain D residue  251 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 95 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 41 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 94 optimal weight:    0.4980
   chunk 98 optimal weight:    0.8980
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3732 r_free = 0.3732 target = 0.148577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.113822 restraints weight = 31336.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 1.92
r_work: 0.3257 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9884  Z= 0.124
  Angle     :  0.479   4.674  13392  Z= 0.252
  Chirality :  0.041   0.143   1580
  Planarity :  0.005   0.038   1704
  Dihedral  :  3.939  26.007   1368
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 10.78 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.25), residues: 1232
  helix:  2.72 (0.20), residues: 676
  sheet:  1.26 (0.40), residues: 168
  loop : -1.75 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP D  41 
 HIS   0.003   0.001   HIS A  90 
 PHE   0.008   0.001   PHE B 309 
 TYR   0.006   0.001   TYR B 159 
 ARG   0.001   0.000   ARG C 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05593 (  576)
  hydrogen bonds       : angle       4.17228 ( 1716)
  covalent geometry    : bond        0.00275 ( 9884)
  covalent geometry    : angle       0.47869 (13392)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 13175.97 seconds
wall clock time: 225 minutes 25.46 seconds (13525.46 seconds total)