Starting phenix.real_space_refine
on Fri Aug 22 21:59:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wca_37436/08_2025/8wca_37436_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wca_37436/08_2025/8wca_37436.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.48
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wca_37436/08_2025/8wca_37436_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wca_37436/08_2025/8wca_37436_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wca_37436/08_2025/8wca_37436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wca_37436/08_2025/8wca_37436.map"
  }
  resolution = 3.48
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.078
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      55      5.16       5
     C    5232      2.51       5
     N    1374      2.21       5
     O    1499      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8160
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 327, 2336
          Classifications: {'peptide': 327}
          Incomplete info: {'truncation_to_alanine': 45}
          Link IDs: {'PTRANS': 5, 'TRANS': 321}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 176
          Unresolved non-hydrogen angles: 217
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 4, 'ARG:plan': 11, 'ASP:plan': 9, 'HIS:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 127
    Chain: "C"
      Number of atoms: 1799
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1799
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 225}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 142
          Unresolved non-hydrogen dihedrals: 97
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 7, 'GLN:plan1': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 69
    Chain: "R"
      Number of atoms: 2010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2010
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 11, 'TRANS': 261}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 229
          Unresolved non-hydrogen angles: 282
          Unresolved non-hydrogen dihedrals: 198
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 2, 'HIS:plan': 6, 'ASP:plan': 2, 'GLU:plan': 5, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 97
    Chain: "S"
      Number of atoms: 1666
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1666
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 25}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 125
          Unresolved non-hydrogen dihedrals: 84
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'GLU:plan': 6, 'ASP:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 70
    Chain: "Y"
      Number of atoms: 340
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 340
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "R"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'PEA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.61, per 1000 atoms: 0.20
  Number of scatterers: 8160
  At special positions: 0
  Unit cell: (103.96, 117.76, 124.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      55     16.00
     O    1499      8.00
     N    1374      7.00
     C    5232      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  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: 0.42
  Conformation dependent library (CDL) restraints added in 394.9 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 15 sheets defined
      37.3% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'B' and resid 13 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'C' and resid 6 through 20
      removed outlier: 3.692A  pdb=" N   LYS C  10 " --> pdb=" O   SER C   6 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ALA C  11 " --> pdb=" O   ALA C   7 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 22 through 32
      removed outlier: 3.511A  pdb=" N   ASP C  26 " --> pdb=" O   GLN C  22 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA C  32 " --> pdb=" O   GLN C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 54
      removed outlier: 3.536A  pdb=" N   ARG C  54 " --> pdb=" O   VAL C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 216
      removed outlier: 3.715A  pdb=" N   ASN C 216 " --> pdb=" O   GLN C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 233 through 246
    Processing helix  chain 'C' and resid 260 through 270
    Processing helix  chain 'C' and resid 274 through 279
    Processing helix  chain 'C' and resid 280 through 283
      removed outlier: 4.036A  pdb=" N   ALA C 283 " --> pdb=" O   PRO C 280 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 280 through 283'
    Processing helix  chain 'C' and resid 298 through 319
      removed outlier: 4.062A  pdb=" N   ILE C 315 " --> pdb=" O   GLU C 311 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER C 316 " --> pdb=" O   PHE C 312 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   SER C 319 " --> pdb=" O   ILE C 315 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 358
    Processing helix  chain 'R' and resid 23 through 47
    Processing helix  chain 'R' and resid 59 through 85
      removed outlier: 3.734A  pdb=" N   HIS R  63 " --> pdb=" O   ASN R  59 " (cutoff:3.500A)
      Proline residue:  R  78  - end of helix
      removed outlier: 4.496A  pdb=" N   ALA R  85 " --> pdb=" O   MET R  81 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 96 through 125
      removed outlier: 4.267A  pdb=" N   SER R 107 " --> pdb=" O   ASP R 103 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   SER R 108 " --> pdb=" O   ILE R 104 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   VAL R 125 " --> pdb=" O   ARG R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 129
      No H-bonds generated for 'chain 'R' and resid 127 through 129'
    Processing helix  chain 'R' and resid 130 through 135
      removed outlier: 3.610A  pdb=" N   LYS R 134 " --> pdb=" O   ARG R 130 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 136 through 161
      Proline residue:  R 151  - end of helix
    Processing helix  chain 'R' and resid 168 through 179
    Processing helix  chain 'R' and resid 187 through 199
      removed outlier: 3.784A  pdb=" N   VAL R 192 " --> pdb=" O   LYS R 188 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU R 193 " --> pdb=" O   ILE R 189 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 199 through 224
      removed outlier: 4.090A  pdb=" N   CYS R 208 " --> pdb=" O   SER R 204 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 248 through 277
      removed outlier: 3.889A  pdb=" N   THR R 252 " --> pdb=" O   LYS R 248 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU R 253 " --> pdb=" O   ALA R 249 " (cutoff:3.500A)
      Proline residue:  R 266  - end of helix
      Proline residue:  R 275  - end of helix
    Processing helix  chain 'R' and resid 282 through 307
      removed outlier: 3.727A  pdb=" N   ASN R 286 " --> pdb=" O   PRO R 282 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   VAL R 288 " --> pdb=" O   THR R 284 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   SER R 297 " --> pdb=" O   GLY R 293 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR R 298 " --> pdb=" O   TYR R 294 " (cutoff:3.500A)
      Proline residue:  R 301  - end of helix
      removed outlier: 3.555A  pdb=" N   PHE R 307 " --> pdb=" O   VAL R 303 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 308 through 319
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.649A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.920A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 16 through 25
      removed outlier: 3.890A  pdb=" N   ILE Y  25 " --> pdb=" O   MET Y  21 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 29 through 45
      removed outlier: 3.923A  pdb=" N   ALA Y  33 " --> pdb=" O   LYS Y  29 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ALA Y  34 " --> pdb=" O   VAL Y  30 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.956A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 102 through 105
      removed outlier: 5.902A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 146 through 151
      removed outlier: 4.384A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.107A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.761A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 229 through 234
    Processing sheet with id=AA6, first strand: chain 'B' and resid 276 through 277
      removed outlier: 6.798A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.253A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 5.018A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 315 through 317
      removed outlier: 6.893A  pdb=" N   GLY B 330 " --> pdb=" O   SER B 316 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   VAL B 327 " --> pdb=" O   TRP B 339 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 184 through 185
    Processing sheet with id=AA9, first strand: chain 'C' and resid 184 through 185
      removed outlier: 4.332A  pdb=" N   VAL C 201 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA C 220 " --> pdb=" O   ARG C  35 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL C 225 " --> pdb=" O   PHE C 257 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   VAL C 254 " --> pdb=" O   TYR C 327 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
      removed outlier: 3.684A  pdb=" N   GLN S   3 " --> pdb=" O   SER S  25 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   SER S  25 " --> pdb=" O   GLN S   3 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 10 through 11
      removed outlier: 5.957A  pdb=" N   GLY S  10 " --> pdb=" O   THR S 118 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'S' and resid 45 through 51
      removed outlier: 6.689A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB5, first strand: chain 'S' and resid 146 through 148
      removed outlier: 3.692A  pdb=" N   GLU S 246 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'S' and resid 194 through 195
      removed outlier: 3.719A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1113 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: 0.79

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.14 -     1.27: 1300
        1.27 -     1.41: 2226
        1.41 -     1.54: 4705
        1.54 -     1.68: 35
        1.68 -     1.81: 81
  Bond restraints: 8347
  Sorted by residual:
  bond pdb=" C   ASN R  41 "
       pdb=" O   ASN R  41 "
    ideal  model  delta    sigma   weight residual
    1.236  1.138  0.099 1.26e-02 6.30e+03 6.13e+01
  bond pdb=" C   ARG C 356 "
       pdb=" O   ARG C 356 "
    ideal  model  delta    sigma   weight residual
    1.236  1.143  0.093 1.31e-02 5.83e+03 5.06e+01
  bond pdb=" CA  ARG C 356 "
       pdb=" C   ARG C 356 "
    ideal  model  delta    sigma   weight residual
    1.520  1.423  0.097 1.39e-02 5.18e+03 4.91e+01
  bond pdb=" CA  ASN R  41 "
       pdb=" C   ASN R  41 "
    ideal  model  delta    sigma   weight residual
    1.523  1.438  0.085 1.35e-02 5.49e+03 3.92e+01
  bond pdb=" C   ARG B  49 "
       pdb=" O   ARG B  49 "
    ideal  model  delta    sigma   weight residual
    1.235  1.175  0.060 1.00e-02 1.00e+04 3.55e+01
  ... (remaining 8342 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 11089
        2.44 -     4.88: 233
        4.88 -     7.32: 46
        7.32 -     9.76: 10
        9.76 -    12.20: 8
  Bond angle restraints: 11386
  Sorted by residual:
  angle pdb=" N   CYS R  96 "
        pdb=" CA  CYS R  96 "
        pdb=" C   CYS R  96 "
      ideal   model   delta    sigma   weight residual
     113.43  101.23   12.20 1.26e+00 6.30e-01 9.37e+01
  angle pdb=" N   GLY R  92 "
        pdb=" CA  GLY R  92 "
        pdb=" C   GLY R  92 "
      ideal   model   delta    sigma   weight residual
     111.93  122.92  -10.99 1.15e+00 7.56e-01 9.13e+01
  angle pdb=" N   LEU B  55 "
        pdb=" CA  LEU B  55 "
        pdb=" C   LEU B  55 "
      ideal   model   delta    sigma   weight residual
     111.07  118.67   -7.60 1.07e+00 8.73e-01 5.04e+01
  angle pdb=" N   ARG C 356 "
        pdb=" CA  ARG C 356 "
        pdb=" C   ARG C 356 "
      ideal   model   delta    sigma   weight residual
     114.31  105.32    8.99 1.29e+00 6.01e-01 4.85e+01
  angle pdb=" N   VAL R 192 "
        pdb=" CA  VAL R 192 "
        pdb=" C   VAL R 192 "
      ideal   model   delta    sigma   weight residual
     110.42  103.94    6.48 9.60e-01 1.09e+00 4.56e+01
  ... (remaining 11381 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4452
       17.98 -    35.97: 305
       35.97 -    53.95: 64
       53.95 -    71.93: 6
       71.93 -    89.92: 6
  Dihedral angle restraints: 4833
    sinusoidal: 1604
      harmonic: 3229
  Sorted by residual:
  dihedral pdb=" N   LEU R 193 "
           pdb=" C   LEU R 193 "
           pdb=" CA  LEU R 193 "
           pdb=" CB  LEU R 193 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.87  -12.07     0      2.50e+00 1.60e-01 2.33e+01
  dihedral pdb=" C   ARG B  49 "
           pdb=" N   ARG B  49 "
           pdb=" CA  ARG B  49 "
           pdb=" CB  ARG B  49 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -110.73  -11.87     0      2.50e+00 1.60e-01 2.25e+01
  dihedral pdb=" C   TYR R  90 "
           pdb=" N   TYR R  90 "
           pdb=" CA  TYR R  90 "
           pdb=" CB  TYR R  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -111.10  -11.50     0      2.50e+00 1.60e-01 2.12e+01
  ... (remaining 4830 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 1272
       0.120 -    0.240: 40
       0.240 -    0.361: 6
       0.361 -    0.481: 2
       0.481 -    0.601: 3
  Chirality restraints: 1323
  Sorted by residual:
  chirality pdb=" CA  LEU R 193 "
            pdb=" N   LEU R 193 "
            pdb=" C   LEU R 193 "
            pdb=" CB  LEU R 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 9.03e+00
  chirality pdb=" CA  ASN R  41 "
            pdb=" N   ASN R  41 "
            pdb=" C   ASN R  41 "
            pdb=" CB  ASN R  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.00e+00
  chirality pdb=" CA  SER R 198 "
            pdb=" N   SER R 198 "
            pdb=" C   SER R 198 "
            pdb=" CB  SER R 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.46e+00
  ... (remaining 1320 not shown)

  Planarity restraints: 1443
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  35 "   -0.024 2.00e-02 2.50e+03   4.80e-02 2.31e+01
        pdb=" C   LEU R  35 "    0.083 2.00e-02 2.50e+03
        pdb=" O   LEU R  35 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   THR R  36 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 355 "   -0.024 2.00e-02 2.50e+03   4.78e-02 2.28e+01
        pdb=" C   LEU C 355 "    0.083 2.00e-02 2.50e+03
        pdb=" O   LEU C 355 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ARG C 356 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS R  96 "    0.022 2.00e-02 2.50e+03   4.29e-02 1.84e+01
        pdb=" C   CYS R  96 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   CYS R  96 "    0.027 2.00e-02 2.50e+03
        pdb=" N   LYS R  97 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1440 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 158
        2.66 -     3.22: 7534
        3.22 -     3.78: 11823
        3.78 -     4.34: 15482
        4.34 -     4.90: 26720
  Nonbonded interactions: 61717
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.105 3.040
  nonbonded pdb=" OD1 ASN R 296 "
            pdb=" ND2 ASN R 300 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" OD1 ASP B 163 "
            pdb=" OG1 THR B 165 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OE2 GLU C  14 "
            pdb=" OG  SER S  52 "
     model   vdw
     2.225 3.040
  nonbonded pdb=" O   SER R 198 "
            pdb=" OG  SER R 198 "
     model   vdw
     2.243 3.040
  ... (remaining 61712 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: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.230
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.000
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
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      :  0.006   0.099   8349  Z= 0.420
  Angle     :  0.875  12.199  11390  Z= 0.542
  Chirality :  0.063   0.601   1323
  Planarity :  0.006   0.090   1443
  Dihedral  : 13.523  89.915   2741
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  0.89 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.48 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.26), residues: 1088
  helix:  0.83 (0.29), residues: 372
  sheet:  0.07 (0.34), residues: 267
  loop : -1.39 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG S  98 
 TYR   0.017   0.001   TYR R  90 
 PHE   0.044   0.002   PHE R 154 
 TRP   0.038   0.002   TRP R 291 
 HIS   0.006   0.001   HIS B 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00639 ( 8347)
  covalent geometry    : angle       0.87477 (11386)
  SS BOND              : bond        0.00465 (    2)
  SS BOND              : angle       0.37887 (    4)
  hydrogen bonds       : bond        0.14082 (  381)
  hydrogen bonds       : angle       6.38334 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 155
  time to evaluate  : 0.222 
Fit side-chains
REVERT: B  251 ARG cc_start: 0.7651 (mmt90) cc_final: 0.7359 (mmt-90)
REVERT: C   22 GLN cc_start: 0.8398 (tp40) cc_final: 0.7978 (tp40)
REVERT: C  345 ASP cc_start: 0.7465 (m-30) cc_final: 0.7262 (m-30)
REVERT: S    5 VAL cc_start: 0.7306 (t) cc_final: 0.7045 (p)
  outliers start: 7
  outliers final: 5
  residues processed: 160
  average time/residue: 0.0733
  time to fit residues: 16.4679
Evaluate side-chains
  121 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   89 TRP
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  154 PHE
Chi-restraints excluded: chain R residue  185 PHE
Chi-restraints excluded: chain R residue  194 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.5980
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
C 238 ASN
C 259 ASN
S 179 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.200161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.164098 restraints weight = 9378.487|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 2.20
r_work: 0.3658 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.3515 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8349  Z= 0.168
  Angle     :  0.635  11.203  11390  Z= 0.333
  Chirality :  0.046   0.148   1323
  Planarity :  0.005   0.061   1443
  Dihedral  :  5.509  63.407   1194
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.42 %
    Favored  : 87.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.13 (0.26), residues: 1088
  helix:  1.27 (0.27), residues: 373
  sheet: -0.02 (0.34), residues: 271
  loop : -1.28 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG S  98 
 TYR   0.016   0.002   TYR S 190 
 PHE   0.013   0.002   PHE R 268 
 TRP   0.025   0.002   TRP R 291 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 8347)
  covalent geometry    : angle       0.63486 (11386)
  SS BOND              : bond        0.00655 (    2)
  SS BOND              : angle       0.71791 (    4)
  hydrogen bonds       : bond        0.05271 (  381)
  hydrogen bonds       : angle       4.88623 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.204 
Fit side-chains
REVERT: B  251 ARG cc_start: 0.8029 (mmt90) cc_final: 0.7800 (mmt-90)
REVERT: C   22 GLN cc_start: 0.8809 (tp40) cc_final: 0.8456 (tp40)
REVERT: C  292 THR cc_start: 0.8766 (m) cc_final: 0.8553 (p)
REVERT: C  345 ASP cc_start: 0.7700 (m-30) cc_final: 0.7295 (m-30)
REVERT: C  359 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8729 (mt-10)
REVERT: S  113 GLN cc_start: 0.8662 (tp40) cc_final: 0.8377 (mm-40)
REVERT: S  204 SER cc_start: 0.7925 (m) cc_final: 0.7703 (t)
  outliers start: 16
  outliers final: 15
  residues processed: 138
  average time/residue: 0.0623
  time to fit residues: 12.4499
Evaluate side-chains
  141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 125
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  195 ASN
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain R residue   89 TRP
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  219 GLU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  214 LEU
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 39 optimal weight:    6.9990
   chunk 64 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 0 optimal weight:   70.0000
   chunk 26 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 46 optimal weight:   20.0000
   chunk 68 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
R 113 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.198530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.161778 restraints weight = 9305.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3895 rms_B_bonded: 2.15
r_work: 0.3640 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3500 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   8349  Z= 0.168
  Angle     :  0.605  10.458  11390  Z= 0.319
  Chirality :  0.046   0.145   1323
  Planarity :  0.004   0.045   1443
  Dihedral  :  5.084  51.843   1189
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.10 %
    Favored  : 83.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.26), residues: 1088
  helix:  1.65 (0.27), residues: 370
  sheet: -0.13 (0.34), residues: 277
  loop : -1.34 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 347 
 TYR   0.015   0.002   TYR R 304 
 PHE   0.015   0.002   PHE R 268 
 TRP   0.020   0.002   TRP R 291 
 HIS   0.006   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 ( 8347)
  covalent geometry    : angle       0.60453 (11386)
  SS BOND              : bond        0.00644 (    2)
  SS BOND              : angle       0.66274 (    4)
  hydrogen bonds       : bond        0.05133 (  381)
  hydrogen bonds       : angle       4.73281 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.257 
Fit side-chains
REVERT: C   22 GLN cc_start: 0.8781 (tp40) cc_final: 0.8433 (tp40)
REVERT: C  292 THR cc_start: 0.8763 (m) cc_final: 0.8474 (p)
REVERT: C  345 ASP cc_start: 0.7660 (m-30) cc_final: 0.7193 (m-30)
REVERT: C  359 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8617 (mt-10)
REVERT: S  113 GLN cc_start: 0.8704 (tp40) cc_final: 0.8428 (mm-40)
REVERT: S  140 MET cc_start: 0.7777 (mmm) cc_final: 0.6860 (mmm)
  outliers start: 17
  outliers final: 13
  residues processed: 136
  average time/residue: 0.0755
  time to fit residues: 14.6828
Evaluate side-chains
  138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 124
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  195 ASN
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  219 GLU
Chi-restraints excluded: chain R residue  272 VAL
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 75 optimal weight:    4.9990
   chunk 52 optimal weight:    7.9990
   chunk 38 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 0 optimal weight:   70.0000
   chunk 58 optimal weight:    0.0040
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.5998

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

Flipped N/Q/H residues before XYZ refinement:
B 340 ASN
C 238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.197758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.161992 restraints weight = 9470.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3901 rms_B_bonded: 2.35
r_work: 0.3623 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8349  Z= 0.169
  Angle     :  0.607  10.581  11390  Z= 0.319
  Chirality :  0.045   0.150   1323
  Planarity :  0.004   0.035   1443
  Dihedral  :  4.502  40.800   1186
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.50 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.07 (0.26), residues: 1088
  helix:  1.82 (0.27), residues: 368
  sheet: -0.13 (0.34), residues: 275
  loop : -1.37 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 314 
 TYR   0.015   0.002   TYR S 190 
 PHE   0.015   0.002   PHE R 268 
 TRP   0.020   0.002   TRP R 291 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 8347)
  covalent geometry    : angle       0.60700 (11386)
  SS BOND              : bond        0.00603 (    2)
  SS BOND              : angle       0.68676 (    4)
  hydrogen bonds       : bond        0.05079 (  381)
  hydrogen bonds       : angle       4.70851 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.187 
Fit side-chains
REVERT: C   22 GLN cc_start: 0.8742 (tp40) cc_final: 0.8426 (tp40)
REVERT: C  345 ASP cc_start: 0.7543 (m-30) cc_final: 0.7187 (m-30)
REVERT: C  359 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8485 (mt-10)
REVERT: S  113 GLN cc_start: 0.8688 (tp40) cc_final: 0.8409 (mm-40)
REVERT: S  192 MET cc_start: 0.8613 (tmm) cc_final: 0.8357 (tmm)
  outliers start: 20
  outliers final: 16
  residues processed: 137
  average time/residue: 0.0682
  time to fit residues: 13.6855
Evaluate side-chains
  138 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  195 ASN
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain R residue   89 TRP
Chi-restraints excluded: chain R residue   96 CYS
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  219 GLU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 31 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 83 optimal weight:    0.1980
   chunk 23 optimal weight:    5.9990
   overall best weight:    1.8388

-------------------------------------------------------------------------------
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 = 0.4230 r_free = 0.4230 target = 0.196219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.160583 restraints weight = 9433.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 2.11
r_work: 0.3620 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.1999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8349  Z= 0.185
  Angle     :  0.612  10.361  11390  Z= 0.325
  Chirality :  0.046   0.143   1323
  Planarity :  0.004   0.037   1443
  Dihedral  :  4.493  33.444   1186
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 16.14 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.26), residues: 1088
  helix:  1.83 (0.27), residues: 368
  sheet: -0.21 (0.33), residues: 275
  loop : -1.40 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 347 
 TYR   0.020   0.002   TYR B 105 
 PHE   0.018   0.002   PHE R 268 
 TRP   0.020   0.002   TRP R 310 
 HIS   0.006   0.002   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 8347)
  covalent geometry    : angle       0.61163 (11386)
  SS BOND              : bond        0.00607 (    2)
  SS BOND              : angle       0.66795 (    4)
  hydrogen bonds       : bond        0.05280 (  381)
  hydrogen bonds       : angle       4.75237 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 121
  time to evaluate  : 0.230 
Fit side-chains
REVERT: C   22 GLN cc_start: 0.8828 (tp40) cc_final: 0.8559 (tp40)
REVERT: C  345 ASP cc_start: 0.7617 (m-30) cc_final: 0.7255 (m-30)
REVERT: C  359 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8549 (mt-10)
REVERT: R  257 MET cc_start: 0.7485 (mmt) cc_final: 0.7166 (mmm)
REVERT: S  113 GLN cc_start: 0.8720 (tp40) cc_final: 0.8434 (mm-40)
REVERT: S  140 MET cc_start: 0.7877 (mmm) cc_final: 0.6902 (mmm)
REVERT: S  192 MET cc_start: 0.8813 (tmm) cc_final: 0.8568 (tmm)
  outliers start: 28
  outliers final: 18
  residues processed: 137
  average time/residue: 0.0707
  time to fit residues: 14.0200
Evaluate side-chains
  139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  195 ASN
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  308 ILE
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain R residue   89 TRP
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  219 GLU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 38 optimal weight:    0.0070
   chunk 34 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 98 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 55 optimal weight:   30.0000
   chunk 70 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
B 183 HIS
C 238 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.200270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.164409 restraints weight = 9261.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3919 rms_B_bonded: 2.14
r_work: 0.3662 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work: 0.3516 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8349  Z= 0.121
  Angle     :  0.552   8.860  11390  Z= 0.292
  Chirality :  0.044   0.160   1323
  Planarity :  0.004   0.040   1443
  Dihedral  :  4.195  26.774   1186
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.92 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.26), residues: 1088
  helix:  2.13 (0.28), residues: 366
  sheet: -0.08 (0.33), residues: 279
  loop : -1.35 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 314 
 TYR   0.014   0.001   TYR R 172 
 PHE   0.013   0.001   PHE S  68 
 TRP   0.024   0.002   TRP R 310 
 HIS   0.003   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8347)
  covalent geometry    : angle       0.55245 (11386)
  SS BOND              : bond        0.00561 (    2)
  SS BOND              : angle       0.61986 (    4)
  hydrogen bonds       : bond        0.04360 (  381)
  hydrogen bonds       : angle       4.53860 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 0.313 
Fit side-chains
REVERT: C   22 GLN cc_start: 0.8695 (tp40) cc_final: 0.8423 (tp40)
REVERT: C  186 GLU cc_start: 0.7934 (tp30) cc_final: 0.7609 (tp30)
REVERT: C  247 ARG cc_start: 0.8440 (ppt170) cc_final: 0.8208 (ptm-80)
REVERT: C  359 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8529 (mt-10)
REVERT: R  257 MET cc_start: 0.7451 (mmt) cc_final: 0.7210 (mmm)
REVERT: S  113 GLN cc_start: 0.8686 (tp40) cc_final: 0.8376 (mm-40)
REVERT: S  192 MET cc_start: 0.8789 (tmm) cc_final: 0.8513 (tmm)
  outliers start: 23
  outliers final: 18
  residues processed: 142
  average time/residue: 0.0680
  time to fit residues: 13.7499
Evaluate side-chains
  140 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  195 ASN
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  219 GLU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  214 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:   30.0000
   chunk 105 optimal weight:    0.0570
   chunk 65 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    0.9100

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

Flipped N/Q/H residues before XYZ refinement:
B 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.200775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.164862 restraints weight = 9349.474|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 2.12
r_work: 0.3666 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3523 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8349  Z= 0.123
  Angle     :  0.556   8.450  11390  Z= 0.294
  Chirality :  0.044   0.181   1323
  Planarity :  0.004   0.043   1443
  Dihedral  :  4.086  21.475   1186
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.04 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.26), residues: 1088
  helix:  2.19 (0.27), residues: 366
  sheet: -0.11 (0.33), residues: 281
  loop : -1.32 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 314 
 TYR   0.013   0.001   TYR B 105 
 PHE   0.011   0.001   PHE R 165 
 TRP   0.026   0.002   TRP R 310 
 HIS   0.004   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8347)
  covalent geometry    : angle       0.55592 (11386)
  SS BOND              : bond        0.00557 (    2)
  SS BOND              : angle       0.59855 (    4)
  hydrogen bonds       : bond        0.04337 (  381)
  hydrogen bonds       : angle       4.49134 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 122
  time to evaluate  : 0.214 
Fit side-chains
REVERT: C   22 GLN cc_start: 0.8683 (tp40) cc_final: 0.8407 (tp40)
REVERT: C  186 GLU cc_start: 0.7934 (tp30) cc_final: 0.7639 (tp30)
REVERT: C  247 ARG cc_start: 0.8431 (ppt170) cc_final: 0.8200 (ptm-80)
REVERT: C  359 GLU cc_start: 0.9050 (OUTLIER) cc_final: 0.8505 (mt-10)
REVERT: R  257 MET cc_start: 0.7381 (mmt) cc_final: 0.7151 (mmm)
REVERT: S  113 GLN cc_start: 0.8674 (tp40) cc_final: 0.8358 (mm-40)
REVERT: S  140 MET cc_start: 0.7850 (mmm) cc_final: 0.6822 (mmm)
REVERT: S  192 MET cc_start: 0.8787 (tmm) cc_final: 0.8492 (tmm)
  outliers start: 27
  outliers final: 22
  residues processed: 138
  average time/residue: 0.0635
  time to fit residues: 12.4166
Evaluate side-chains
  142 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 119
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  195 ASN
Chi-restraints excluded: chain C residue  217 ASP
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  213 ILE
Chi-restraints excluded: chain R residue  219 GLU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 103 optimal weight:    0.7980
   chunk 92 optimal weight:    3.9990
   chunk 99 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 21 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 88 optimal weight:    5.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.194415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.157980 restraints weight = 9285.339|
|-----------------------------------------------------------------------------|
r_work (start): 0.3856 rms_B_bonded: 2.27
r_work: 0.3576 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.3429 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   8349  Z= 0.241
  Angle     :  0.667  10.412  11390  Z= 0.355
  Chirality :  0.048   0.189   1323
  Planarity :  0.004   0.050   1443
  Dihedral  :  4.496  22.269   1186
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 18.55 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.26), residues: 1088
  helix:  1.86 (0.27), residues: 366
  sheet: -0.22 (0.33), residues: 275
  loop : -1.51 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 347 
 TYR   0.035   0.002   TYR B 105 
 PHE   0.020   0.002   PHE R 268 
 TRP   0.026   0.002   TRP R 310 
 HIS   0.008   0.002   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 ( 8347)
  covalent geometry    : angle       0.66707 (11386)
  SS BOND              : bond        0.00593 (    2)
  SS BOND              : angle       0.69509 (    4)
  hydrogen bonds       : bond        0.05839 (  381)
  hydrogen bonds       : angle       4.92361 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 118
  time to evaluate  : 0.310 
Fit side-chains
REVERT: C   39 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8199 (mp)
REVERT: C  186 GLU cc_start: 0.7989 (tp30) cc_final: 0.7636 (tp30)
REVERT: C  247 ARG cc_start: 0.8507 (ppt170) cc_final: 0.8251 (ptm-80)
REVERT: C  313 LEU cc_start: 0.7966 (mm) cc_final: 0.7630 (mm)
REVERT: C  345 ASP cc_start: 0.7712 (m-30) cc_final: 0.7337 (m-30)
REVERT: C  359 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8420 (mt-10)
REVERT: R  257 MET cc_start: 0.7648 (mmt) cc_final: 0.7307 (mmm)
REVERT: S  113 GLN cc_start: 0.8723 (tp40) cc_final: 0.8442 (mm-40)
REVERT: S  192 MET cc_start: 0.8807 (tmm) cc_final: 0.8528 (tmm)
REVERT: S  204 SER cc_start: 0.8022 (m) cc_final: 0.7709 (t)
  outliers start: 27
  outliers final: 22
  residues processed: 135
  average time/residue: 0.0715
  time to fit residues: 13.8325
Evaluate side-chains
  141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   39 LEU
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  195 ASN
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain R residue   89 TRP
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  148 TRP
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 100 optimal weight:    6.9990
   chunk 26 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.199964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.163358 restraints weight = 9350.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3910 rms_B_bonded: 2.14
r_work: 0.3655 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   8349  Z= 0.125
  Angle     :  0.581  11.195  11390  Z= 0.305
  Chirality :  0.045   0.186   1323
  Planarity :  0.004   0.048   1443
  Dihedral  :  4.175  17.970   1186
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 19.31 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.25 (0.26), residues: 1088
  helix:  2.17 (0.28), residues: 365
  sheet: -0.24 (0.34), residues: 279
  loop : -1.27 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 314 
 TYR   0.014   0.001   TYR B 105 
 PHE   0.011   0.001   PHE R 268 
 TRP   0.026   0.002   TRP R 310 
 HIS   0.005   0.001   HIS B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8347)
  covalent geometry    : angle       0.58145 (11386)
  SS BOND              : bond        0.00568 (    2)
  SS BOND              : angle       0.60353 (    4)
  hydrogen bonds       : bond        0.04509 (  381)
  hydrogen bonds       : angle       4.61206 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.237 
Fit side-chains
REVERT: C  186 GLU cc_start: 0.7860 (tp30) cc_final: 0.7583 (tp30)
REVERT: C  247 ARG cc_start: 0.8441 (ppt170) cc_final: 0.8217 (ptm-80)
REVERT: C  359 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8472 (mt-10)
REVERT: R  257 MET cc_start: 0.7446 (mmt) cc_final: 0.7232 (mmm)
REVERT: S  113 GLN cc_start: 0.8694 (tp40) cc_final: 0.8406 (mm-40)
REVERT: S  140 MET cc_start: 0.7879 (mmm) cc_final: 0.6921 (mmm)
REVERT: S  192 MET cc_start: 0.8823 (tmm) cc_final: 0.8541 (tmm)
  outliers start: 24
  outliers final: 19
  residues processed: 136
  average time/residue: 0.0676
  time to fit residues: 13.3484
Evaluate side-chains
  139 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   36 LEU
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  195 ASN
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
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 = 0.4253 r_free = 0.4253 target = 0.198626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.161562 restraints weight = 9300.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3890 rms_B_bonded: 2.24
r_work: 0.3623 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work: 0.3477 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8349  Z= 0.152
  Angle     :  0.605  12.213  11390  Z= 0.317
  Chirality :  0.045   0.205   1323
  Planarity :  0.004   0.049   1443
  Dihedral  :  4.169  16.648   1186
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.31 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.26 (0.26), residues: 1088
  helix:  2.17 (0.27), residues: 364
  sheet: -0.14 (0.33), residues: 275
  loop : -1.32 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 347 
 TYR   0.019   0.001   TYR B 105 
 PHE   0.013   0.001   PHE R 268 
 TRP   0.023   0.002   TRP R 310 
 HIS   0.005   0.001   HIS S  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 8347)
  covalent geometry    : angle       0.60544 (11386)
  SS BOND              : bond        0.00582 (    2)
  SS BOND              : angle       0.58369 (    4)
  hydrogen bonds       : bond        0.04772 (  381)
  hydrogen bonds       : angle       4.64168 ( 1113)

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

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

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2176 Ramachandran restraints generated.
    1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.285 
Fit side-chains
REVERT: C  186 GLU cc_start: 0.7954 (tp30) cc_final: 0.7674 (tp30)
REVERT: C  247 ARG cc_start: 0.8478 (ppt170) cc_final: 0.8235 (ptm-80)
REVERT: C  359 GLU cc_start: 0.9043 (OUTLIER) cc_final: 0.8461 (mt-10)
REVERT: R  257 MET cc_start: 0.7476 (mmt) cc_final: 0.7211 (mmm)
REVERT: S  113 GLN cc_start: 0.8708 (tp40) cc_final: 0.8414 (mm-40)
REVERT: S  140 MET cc_start: 0.7908 (mmm) cc_final: 0.6926 (mmm)
REVERT: S  192 MET cc_start: 0.8813 (tmm) cc_final: 0.8515 (tmm)
  outliers start: 23
  outliers final: 19
  residues processed: 131
  average time/residue: 0.0737
  time to fit residues: 13.6523
Evaluate side-chains
  134 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  183 HIS
Chi-restraints excluded: chain B residue  286 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  315 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   48 THR
Chi-restraints excluded: chain C residue  195 ASN
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  287 THR
Chi-restraints excluded: chain C residue  315 ILE
Chi-restraints excluded: chain C residue  359 GLU
Chi-restraints excluded: chain R residue  126 CYS
Chi-restraints excluded: chain R residue  184 VAL
Chi-restraints excluded: chain R residue  219 GLU
Chi-restraints excluded: chain R residue  290 ILE
Chi-restraints excluded: chain S residue  184 SER
Chi-restraints excluded: chain S residue  238 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 69 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 83 optimal weight:   10.0000
   chunk 56 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.4270 r_free = 0.4270 target = 0.200653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.164379 restraints weight = 9307.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.12
r_work: 0.3661 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.3518 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   8349  Z= 0.126
  Angle     :  0.581  13.016  11390  Z= 0.303
  Chirality :  0.044   0.208   1323
  Planarity :  0.004   0.047   1443
  Dihedral  :  4.010  16.754   1186
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 19.44 %
    Favored  : 77.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.27), residues: 1088
  helix:  2.34 (0.27), residues: 361
  sheet: -0.20 (0.33), residues: 286
  loop : -1.12 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 314 
 TYR   0.015   0.001   TYR B 105 
 PHE   0.021   0.001   PHE R 185 
 TRP   0.024   0.002   TRP R 310 
 HIS   0.003   0.001   HIS B  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 8347)
  covalent geometry    : angle       0.58116 (11386)
  SS BOND              : bond        0.00557 (    2)
  SS BOND              : angle       0.57122 (    4)
  hydrogen bonds       : bond        0.04296 (  381)
  hydrogen bonds       : angle       4.52132 ( 1113)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2016.46 seconds
wall clock time: 35 minutes 2.66 seconds (2102.66 seconds total)