Starting phenix.real_space_refine
on Thu Feb 13 20:15:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7w40_32298/02_2025/7w40_32298.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7w40_32298/02_2025/7w40_32298.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7w40_32298/02_2025/7w40_32298.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7w40_32298/02_2025/7w40_32298.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7w40_32298/02_2025/7w40_32298.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7w40_32298/02_2025/7w40_32298.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      57      5.16       5
     C    5882      2.51       5
     N    1573      2.21       5
     O    1724      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9236
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2280
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 301, 2280
          Classifications: {'peptide': 301}
          Incomplete info: {'truncation_to_alanine': 37}
          Link IDs: {'PTRANS': 14, 'TRANS': 286}
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 2, 'GLU:plan': 4, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 47
    Chain: "B"
      Number of atoms: 2330
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2330
          Classifications: {'peptide': 283}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 275}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 2409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 315, 2409
          Classifications: {'peptide': 315}
          Link IDs: {'PTRANS': 5, 'TRANS': 309}
    Chain: "D"
      Number of atoms: 365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 365
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 4, 'TRANS': 42}
    Chain: "H"
      Number of atoms: 1771
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1771
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 81
          Unusual residues: {'BAL': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Modifications used: {'PEPT-D': 1}
          Link IDs: {'POST-BETA-TRANS': 1, 'PRE-BETA-TRANS': 1, 'TRANS': 6}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'BAL:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 5.60, per 1000 atoms: 0.61
  Number of scatterers: 9236
  At special positions: 0
  Unit cell: (111.54, 112.554, 128.778, 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      57     16.00
     O    1724      8.00
     N    1573      7.00
     C    5882      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 113 " - pdb=" SG  CYS A 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.07
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 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: 2.52
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DPN E   1 "
      Input volumes are d-peptide like
        pdb=" CB  BAL E   6 "
  Number of C-beta restraints generated:  2222

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 14 sheets defined
      39.2% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 69
      Proline residue:  A  44  - end of helix
      removed outlier: 4.306A  pdb=" N   VAL A  49 " --> pdb=" O   ALA A  45 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   CYS A  66 " --> pdb=" O   ILE A  62 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LYS A  69 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 103
      removed outlier: 3.600A  pdb=" N   PHE A  78 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ALA A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      Proline residue:  A  95  - end of helix
    Processing helix  chain 'A' and resid 108 through 144
      removed outlier: 4.061A  pdb=" N   GLY A 112 " --> pdb=" O   PHE A 108 " (cutoff:3.500A)
      Proline residue:  A 117  - end of helix
      removed outlier: 3.523A  pdb=" N   THR A 122 " --> pdb=" O   PHE A 118 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   THR A 132 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 173
    Processing helix  chain 'A' and resid 173 through 178
    Processing helix  chain 'A' and resid 205 through 219
    Processing helix  chain 'A' and resid 219 through 243
      removed outlier: 3.549A  pdb=" N   TYR A 242 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 251
      No H-bonds generated for 'chain 'A' and resid 249 through 251'
    Processing helix  chain 'A' and resid 252 through 290
      removed outlier: 3.717A  pdb=" N   LYS A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE A 273 " --> pdb=" O   PHE A 269 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA A 274 " --> pdb=" O   VAL A 270 " (cutoff:3.500A)
      Proline residue:  A 279  - end of helix
      removed outlier: 3.743A  pdb=" N   LEU A 285 " --> pdb=" O   HIS A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 326
      removed outlier: 3.593A  pdb=" N   ASN A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
      removed outlier: 4.472A  pdb=" N   SER A 315 " --> pdb=" O   ALA A 311 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   CYS A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      Proline residue:  A 319  - end of helix
      removed outlier: 3.847A  pdb=" N   LEU A 322 " --> pdb=" O   ASN A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 337
    Processing helix  chain 'B' and resid 12 through 38
      removed outlier: 3.822A  pdb=" N   ARG B  38 " --> pdb=" O   GLU B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 53
    Processing helix  chain 'B' and resid 54 through 64
    Processing helix  chain 'B' and resid 68 through 88
      removed outlier: 4.687A  pdb=" N   LYS B  77 " --> pdb=" O   ARG B  73 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   LEU B  78 " --> pdb=" O   GLY B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 151
      removed outlier: 3.750A  pdb=" N   GLU B 150 " --> pdb=" O   ARG B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 162
    Processing helix  chain 'B' and resid 175 through 181
    Processing helix  chain 'B' and resid 212 through 216
    Processing helix  chain 'B' and resid 217 through 221
    Processing helix  chain 'B' and resid 233 through 235
      No H-bonds generated for 'chain 'B' and resid 233 through 235'
    Processing helix  chain 'B' and resid 246 through 260
    Processing helix  chain 'B' and resid 261 through 265
    Processing helix  chain 'B' and resid 275 through 286
      removed outlier: 4.434A  pdb=" N   MET B 284 " --> pdb=" O   GLU B 280 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   TYR B 285 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 292
      removed outlier: 4.171A  pdb=" N   TYR B 291 " --> pdb=" O   HIS B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 315
    Processing helix  chain 'B' and resid 335 through 356
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 18 through 23
    Processing helix  chain 'D' and resid 29 through 44
      removed outlier: 3.509A  pdb=" N   ALA D  33 " --> pdb=" O   LYS D  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 220 through 224
    Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 197
      removed outlier: 8.867A  pdb=" N   VAL A 294 " --> pdb=" O   PRO A 183 " (cutoff:3.500A)
      removed outlier: 7.506A  pdb=" N   HIS A 185 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 196
      removed outlier: 6.347A  pdb=" N   LEU B  40 " --> pdb=" O   ARG B 202 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   VAL B 204 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   LEU B  42 " --> pdb=" O   VAL B 204 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   SER B 225 " --> pdb=" O   LYS B  41 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ILE B 226 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   PHE B 272 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   PHE B 228 " --> pdb=" O   PHE B 272 " (cutoff:3.500A)
      removed outlier: 7.515A  pdb=" N   ASN B 274 " --> pdb=" O   PHE B 228 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL B 230 " --> pdb=" O   ASN B 274 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 52
      removed outlier: 6.739A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.697A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   ASP C  83 " --> pdb=" O   LYS C  89 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   LYS C  89 " --> pdb=" O   ASP C  83 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105
      removed outlier: 7.072A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.652A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.947A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151
      removed outlier: 3.660A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.766A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.895A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.273A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.286A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.595A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   CYS C 294 " --> pdb=" O   VAL C 307 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   VAL C 307 " --> pdb=" O   CYS C 294 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   VAL C 296 " --> pdb=" O   ALA C 305 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.730A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.327A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141
    Processing sheet with id=AB5, first strand: chain 'H' and resid 147 through 148
      removed outlier: 3.616A  pdb=" N   GLU H 246 " --> pdb=" O   VAL H 147 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   LEU H 178 " --> pdb=" O   LEU H 187 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   LEU H 187 " --> pdb=" O   LEU H 178 " (cutoff:3.500A)

    454 hydrogen bonds defined for protein.
    1272 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.81

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2015
        1.33 -     1.45: 2197
        1.45 -     1.57: 5142
        1.57 -     1.69: 0
        1.69 -     1.82: 86
  Bond restraints: 9440
  Sorted by residual:
  bond pdb=" CG  TRP E   3 "
       pdb=" CD2 TRP E   3 "
    ideal  model  delta    sigma   weight residual
    1.433  1.333  0.100 1.80e-02 3.09e+03 3.07e+01
  bond pdb=" CB  PHE E   8 "
       pdb=" CG  PHE E   8 "
    ideal  model  delta    sigma   weight residual
    1.502  1.385  0.117 2.30e-02 1.89e+03 2.57e+01
  bond pdb=" CG  HIS E   7 "
       pdb=" ND1 HIS E   7 "
    ideal  model  delta    sigma   weight residual
    1.378  1.324  0.054 1.10e-02 8.26e+03 2.37e+01
  bond pdb=" CB  DPN E   1 "
       pdb=" CG  DPN E   1 "
    ideal  model  delta    sigma   weight residual
    1.502  1.391  0.111 2.30e-02 1.89e+03 2.34e+01
  bond pdb=" C   VAL A 266 "
       pdb=" O   VAL A 266 "
    ideal  model  delta    sigma   weight residual
    1.237  1.292 -0.055 1.17e-02 7.31e+03 2.19e+01
  ... (remaining 9435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 10547
        1.64 -     3.28: 1904
        3.28 -     4.92: 296
        4.92 -     6.56: 40
        6.56 -     8.20: 12
  Bond angle restraints: 12799
  Sorted by residual:
  angle pdb=" N   ASP C 247 "
        pdb=" CA  ASP C 247 "
        pdb=" C   ASP C 247 "
      ideal   model   delta    sigma   weight residual
     110.35  102.15    8.20 1.36e+00 5.41e-01 3.64e+01
  angle pdb=" N   ALA A 176 "
        pdb=" CA  ALA A 176 "
        pdb=" C   ALA A 176 "
      ideal   model   delta    sigma   weight residual
     113.97  106.80    7.17 1.28e+00 6.10e-01 3.14e+01
  angle pdb=" CA  GLY H 114 "
        pdb=" C   GLY H 114 "
        pdb=" O   GLY H 114 "
      ideal   model   delta    sigma   weight residual
     121.88  117.85    4.03 7.80e-01 1.64e+00 2.67e+01
  angle pdb=" N   LEU A 205 "
        pdb=" CA  LEU A 205 "
        pdb=" C   LEU A 205 "
      ideal   model   delta    sigma   weight residual
     113.55  107.06    6.49 1.26e+00 6.30e-01 2.66e+01
  angle pdb=" N   ARG C  48 "
        pdb=" CA  ARG C  48 "
        pdb=" C   ARG C  48 "
      ideal   model   delta    sigma   weight residual
     113.23  106.84    6.39 1.24e+00 6.50e-01 2.65e+01
  ... (remaining 12794 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 5102
       16.73 -    33.46: 405
       33.46 -    50.20: 78
       50.20 -    66.93: 15
       66.93 -    83.66: 2
  Dihedral angle restraints: 5602
    sinusoidal: 2154
      harmonic: 3448
  Sorted by residual:
  dihedral pdb=" C   TYR H 235 "
           pdb=" N   TYR H 235 "
           pdb=" CA  TYR H 235 "
           pdb=" CB  TYR H 235 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.20   17.60     0      2.50e+00 1.60e-01 4.96e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.36   56.64     1      1.00e+01 1.00e-02 4.32e+01
  dihedral pdb=" N   TYR H 235 "
           pdb=" C   TYR H 235 "
           pdb=" CA  TYR H 235 "
           pdb=" CB  TYR H 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.06  -16.26     0      2.50e+00 1.60e-01 4.23e+01
  ... (remaining 5599 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.135: 1285
       0.135 -    0.270: 145
       0.270 -    0.405: 8
       0.405 -    0.540: 0
       0.540 -    0.675: 1
  Chirality restraints: 1439
  Sorted by residual:
  chirality pdb=" CA  TYR H 235 "
            pdb=" N   TYR H 235 "
            pdb=" C   TYR H 235 "
            pdb=" CB  TYR H 235 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.84    0.67 2.00e-01 2.50e+01 1.14e+01
  chirality pdb=" CA  LEU C  79 "
            pdb=" N   LEU C  79 "
            pdb=" C   LEU C  79 "
            pdb=" CB  LEU C  79 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.66e+00
  chirality pdb=" CA  LEU H   4 "
            pdb=" N   LEU H   4 "
            pdb=" C   LEU H   4 "
            pdb=" CB  LEU H   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.52e+00
  ... (remaining 1436 not shown)

  Planarity restraints: 1630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR H 175 "    0.016 2.00e-02 2.50e+03   2.45e-02 1.20e+01
        pdb=" CG  TYR H 175 "   -0.056 2.00e-02 2.50e+03
        pdb=" CD1 TYR H 175 "    0.033 2.00e-02 2.50e+03
        pdb=" CD2 TYR H 175 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR H 175 "   -0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR H 175 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR H 175 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR H 175 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 127 "    0.016 2.00e-02 2.50e+03   3.20e-02 1.02e+01
        pdb=" C   LYS C 127 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   LYS C 127 "    0.021 2.00e-02 2.50e+03
        pdb=" N   THR C 128 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 315 "   -0.014 2.00e-02 2.50e+03   2.92e-02 8.51e+00
        pdb=" C   VAL C 315 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL C 315 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   SER C 316 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1627 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1996
        2.79 -     3.32: 8658
        3.32 -     3.85: 14852
        3.85 -     4.37: 18476
        4.37 -     4.90: 31094
  Nonbonded interactions: 75076
  Sorted by model distance:
  nonbonded pdb=" O   ASP C 333 "
            pdb=" OG  SER C 334 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OD1 ASP C 205 "
            pdb=" OG  SER C 207 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" NE  ARG C 283 "
            pdb=" OD1 ASP C 298 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" O   SER C  67 "
            pdb=" OG  SER C  67 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OG  SER C 281 "
            pdb=" OD2 ASP D  48 "
     model   vdw
     2.341 3.040
  ... (remaining 75071 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.860
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6395
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      :  0.011   0.117   9440  Z= 0.709
  Angle     :  1.288   8.202  12799  Z= 0.929
  Chirality :  0.085   0.675   1439
  Planarity :  0.006   0.053   1630
  Dihedral  : 12.467  83.658   3371
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.58 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  3.84 %
    Favored  : 94.24 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.23), residues: 1162
  helix:  0.42 (0.25), residues: 411
  sheet:  0.10 (0.31), residues: 286
  loop : -1.08 (0.26), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP C  82 
 HIS   0.009   0.002   HIS C 311 
 PHE   0.030   0.003   PHE C 199 
 TYR   0.056   0.003   TYR H 175 
 ARG   0.011   0.001   ARG A 259 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 230
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  326 SER cc_start: 0.5579 (t) cc_final: 0.5323 (m)
REVERT: B   26 ASP cc_start: 0.7878 (m-30) cc_final: 0.7571 (m-30)
REVERT: B   60 ARG cc_start: 0.6721 (ttp80) cc_final: 0.6093 (mmm160)
REVERT: B   83 ILE cc_start: 0.6982 (mp) cc_final: 0.6749 (mp)
REVERT: B  259 ILE cc_start: 0.7714 (pt) cc_final: 0.7487 (pt)
REVERT: B  322 LYS cc_start: 0.7322 (mtpp) cc_final: 0.6755 (tptt)
REVERT: B  332 THR cc_start: 0.7611 (t) cc_final: 0.7183 (m)
REVERT: B  348 ILE cc_start: 0.6745 (mm) cc_final: 0.6509 (mt)
  outliers start: 19
  outliers final: 3
  residues processed: 246
  average time/residue: 1.2319
  time to fit residues: 323.4074
Evaluate side-chains
  146 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 143
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 TYR
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain B residue  296 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.9980
   chunk 87 optimal weight:    0.0020
   chunk 48 optimal weight:    0.9980
   chunk 30 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 46 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 35 optimal weight:    0.6980
   chunk 55 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 105 optimal weight:    4.9990
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
B 327 HIS
C  75 GLN
H 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.212855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.174118 restraints weight = 9557.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.4163 rms_B_bonded: 2.11
r_work: 0.3994 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3854 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6835
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9440  Z= 0.200
  Angle     :  0.640   9.305  12799  Z= 0.335
  Chirality :  0.043   0.294   1439
  Planarity :  0.004   0.049   1630
  Dihedral  :  5.378  46.068   1303
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 13.85 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.24), residues: 1162
  helix:  1.76 (0.24), residues: 418
  sheet:  0.46 (0.30), residues: 289
  loop : -0.95 (0.27), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C  82 
 HIS   0.004   0.001   HIS C  91 
 PHE   0.015   0.002   PHE B 201 
 TYR   0.051   0.002   TYR H 235 
 ARG   0.007   0.001   ARG B  38 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 150
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   23 LYS cc_start: 0.7739 (mptt) cc_final: 0.7198 (mttp)
REVERT: B   60 ARG cc_start: 0.7042 (ttp80) cc_final: 0.5550 (mmp-170)
REVERT: B  202 ARG cc_start: 0.7057 (mtp85) cc_final: 0.6420 (ptm160)
REVERT: B  303 GLN cc_start: 0.6621 (tp40) cc_final: 0.6202 (tp40)
REVERT: C   76 ASP cc_start: 0.7040 (p0) cc_final: 0.5880 (t0)
REVERT: C  129 ARG cc_start: 0.7091 (mtt180) cc_final: 0.6740 (ttt90)
REVERT: C  188 MET cc_start: 0.7140 (mmm) cc_final: 0.6910 (mmp)
REVERT: C  197 ARG cc_start: 0.6871 (mtp85) cc_final: 0.6443 (mmp80)
REVERT: H  244 LYS cc_start: 0.8067 (tttt) cc_final: 0.7824 (ttpp)
  outliers start: 41
  outliers final: 17
  residues processed: 177
  average time/residue: 1.4764
  time to fit residues: 276.7246
Evaluate side-chains
  138 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  199 TYR
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue  183 GLN
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  311 LYS
Chi-restraints excluded: chain C residue   97 SER
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 60 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 43 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
C 142 HIS
H 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.210025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.171413 restraints weight = 9692.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.4149 rms_B_bonded: 1.98
r_work: 0.3979 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3838 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.3050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9440  Z= 0.205
  Angle     :  0.605   8.390  12799  Z= 0.317
  Chirality :  0.043   0.254   1439
  Planarity :  0.004   0.046   1630
  Dihedral  :  5.622  77.104   1303
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 16.18 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.24), residues: 1162
  helix:  2.24 (0.25), residues: 413
  sheet:  0.43 (0.30), residues: 281
  loop : -0.85 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C  82 
 HIS   0.004   0.001   HIS A 182 
 PHE   0.014   0.002   PHE C 253 
 TYR   0.026   0.002   TYR H 235 
 ARG   0.007   0.000   ARG C 314 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 132
  time to evaluate  : 0.947 
Fit side-chains
   revert: symmetry clash
REVERT: A  216 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6905 (tt)
REVERT: B   38 ARG cc_start: 0.7255 (mtp-110) cc_final: 0.7013 (mtp85)
REVERT: B   60 ARG cc_start: 0.7112 (ttp80) cc_final: 0.5631 (mmp-170)
REVERT: B  202 ARG cc_start: 0.7119 (mtp85) cc_final: 0.6472 (ptm160)
REVERT: B  280 GLU cc_start: 0.7908 (tp30) cc_final: 0.7416 (tm-30)
REVERT: B  322 LYS cc_start: 0.7594 (mtpt) cc_final: 0.7137 (mtpp)
REVERT: B  335 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6653 (tp30)
REVERT: C   52 ARG cc_start: 0.7833 (mtt90) cc_final: 0.7568 (mtp85)
REVERT: C   76 ASP cc_start: 0.7372 (p0) cc_final: 0.6952 (p0)
REVERT: C  129 ARG cc_start: 0.7236 (mtt180) cc_final: 0.6926 (ttt90)
REVERT: C  188 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6933 (mmp)
REVERT: C  197 ARG cc_start: 0.6935 (mtp85) cc_final: 0.6541 (mmp80)
REVERT: C  269 ILE cc_start: 0.7081 (OUTLIER) cc_final: 0.6623 (mm)
REVERT: H  192 MET cc_start: 0.7186 (ttp) cc_final: 0.6851 (ttp)
REVERT: H  235 TYR cc_start: 0.4429 (OUTLIER) cc_final: 0.3975 (t80)
REVERT: H  244 LYS cc_start: 0.8001 (tttt) cc_final: 0.7744 (ttpp)
  outliers start: 49
  outliers final: 20
  residues processed: 164
  average time/residue: 1.4409
  time to fit residues: 250.2509
Evaluate side-chains
  145 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue  148 ARG
Chi-restraints excluded: chain B residue  183 GLN
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  188 MET
Chi-restraints excluded: chain C residue  196 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  235 TYR
Chi-restraints excluded: chain E residue    5 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 99 optimal weight:    0.8980
   chunk 63 optimal weight:    0.5980
   chunk 90 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 109 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
C 110 ASN
H 186 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.209701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.167875 restraints weight = 9510.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.4094 rms_B_bonded: 1.96
r_work: 0.3965 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3823 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9440  Z= 0.188
  Angle     :  0.586   7.580  12799  Z= 0.303
  Chirality :  0.042   0.239   1439
  Planarity :  0.004   0.045   1630
  Dihedral  :  5.227  64.758   1300
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 18.00 %
    Favored  : 77.55 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.24), residues: 1162
  helix:  2.37 (0.25), residues: 414
  sheet:  0.57 (0.30), residues: 277
  loop : -0.77 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  82 
 HIS   0.003   0.001   HIS B 218 
 PHE   0.013   0.002   PHE C 199 
 TYR   0.025   0.001   TYR H 235 
 ARG   0.005   0.000   ARG H  18 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 134
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5769 (tt)
REVERT: A  155 MET cc_start: 0.5863 (ttp) cc_final: 0.5566 (ttm)
REVERT: B   38 ARG cc_start: 0.7268 (mtp-110) cc_final: 0.7050 (mtp85)
REVERT: B   60 ARG cc_start: 0.7152 (ttp80) cc_final: 0.5596 (mmp-170)
REVERT: B  202 ARG cc_start: 0.7029 (mtp85) cc_final: 0.6518 (ptm160)
REVERT: B  280 GLU cc_start: 0.7903 (tp30) cc_final: 0.7376 (tm-30)
REVERT: B  322 LYS cc_start: 0.7681 (mtpt) cc_final: 0.7242 (mtpp)
REVERT: C   52 ARG cc_start: 0.7871 (mtt90) cc_final: 0.7594 (mtp85)
REVERT: C   76 ASP cc_start: 0.7211 (p0) cc_final: 0.6722 (p0)
REVERT: C  101 MET cc_start: 0.7707 (OUTLIER) cc_final: 0.7461 (mtp)
REVERT: C  129 ARG cc_start: 0.7309 (mtt180) cc_final: 0.7040 (ttt90)
REVERT: C  188 MET cc_start: 0.7186 (mmm) cc_final: 0.6920 (mmp)
REVERT: C  197 ARG cc_start: 0.6957 (mtp85) cc_final: 0.6611 (mmp80)
REVERT: C  269 ILE cc_start: 0.7082 (OUTLIER) cc_final: 0.6587 (mm)
REVERT: H  186 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7577 (pp30)
REVERT: H  235 TYR cc_start: 0.4624 (OUTLIER) cc_final: 0.4204 (t80)
REVERT: H  244 LYS cc_start: 0.8165 (tttt) cc_final: 0.7914 (ttpp)
  outliers start: 44
  outliers final: 24
  residues processed: 161
  average time/residue: 1.3604
  time to fit residues: 232.7291
Evaluate side-chains
  147 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 118
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  199 TYR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  183 GLN
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  235 TYR
Chi-restraints excluded: chain E residue    5 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 65 optimal weight:    0.0020
   chunk 34 optimal weight:    0.0470
   chunk 61 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.5486

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
H 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.209921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.168045 restraints weight = 9606.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 1.99
r_work: 0.3977 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3837 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.3638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9440  Z= 0.177
  Angle     :  0.571   7.509  12799  Z= 0.295
  Chirality :  0.042   0.229   1439
  Planarity :  0.004   0.043   1630
  Dihedral  :  5.076  56.487   1300
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 19.21 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.25), residues: 1162
  helix:  2.31 (0.25), residues: 420
  sheet:  0.63 (0.31), residues: 276
  loop : -0.73 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  82 
 HIS   0.003   0.001   HIS C 183 
 PHE   0.013   0.001   PHE C 199 
 TYR   0.025   0.001   TYR B 285 
 ARG   0.006   0.000   ARG H  18 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 123
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 ILE cc_start: 0.6050 (OUTLIER) cc_final: 0.5683 (tt)
REVERT: A  155 MET cc_start: 0.5798 (ttp) cc_final: 0.5529 (ttm)
REVERT: A  298 MET cc_start: 0.6117 (tpp) cc_final: 0.5794 (tpt)
REVERT: B   60 ARG cc_start: 0.7094 (ttp80) cc_final: 0.5613 (mmp-170)
REVERT: B  202 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6452 (ptm160)
REVERT: B  280 GLU cc_start: 0.7918 (tp30) cc_final: 0.7249 (tm-30)
REVERT: B  281 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6122 (mp0)
REVERT: B  335 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6678 (tp30)
REVERT: C   52 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7587 (mtp85)
REVERT: C  129 ARG cc_start: 0.7340 (mtt180) cc_final: 0.7096 (ttt90)
REVERT: C  188 MET cc_start: 0.7189 (mmm) cc_final: 0.6925 (mmp)
REVERT: C  269 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6510 (mm)
REVERT: H  186 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7313 (pp30)
REVERT: H  218 ARG cc_start: 0.7203 (ttp-170) cc_final: 0.6990 (tmm160)
REVERT: H  235 TYR cc_start: 0.4541 (OUTLIER) cc_final: 0.4136 (t80)
REVERT: H  244 LYS cc_start: 0.8193 (tttt) cc_final: 0.7974 (ttpp)
  outliers start: 40
  outliers final: 26
  residues processed: 149
  average time/residue: 1.4900
  time to fit residues: 234.9464
Evaluate side-chains
  145 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  199 TYR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  148 ARG
Chi-restraints excluded: chain B residue  183 GLN
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  196 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  186 GLN
Chi-restraints excluded: chain H residue  188 LEU
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  235 TYR
Chi-restraints excluded: chain E residue    5 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 113 optimal weight:    4.9990
   chunk 103 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0030
   chunk 63 optimal weight:    0.8980
   chunk 5 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9990
   chunk 92 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
** B 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.208520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.166586 restraints weight = 9507.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 1.97
r_work: 0.3948 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3806 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9440  Z= 0.194
  Angle     :  0.586   8.401  12799  Z= 0.302
  Chirality :  0.042   0.234   1439
  Planarity :  0.004   0.043   1630
  Dihedral  :  4.996  54.221   1300
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 20.02 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.25), residues: 1162
  helix:  2.37 (0.25), residues: 414
  sheet:  0.55 (0.30), residues: 282
  loop : -0.68 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS C 183 
 PHE   0.015   0.001   PHE C 199 
 TYR   0.024   0.001   TYR H 235 
 ARG   0.009   0.001   ARG B  38 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 123
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5688 (tt)
REVERT: A  155 MET cc_start: 0.5804 (ttp) cc_final: 0.5541 (ttm)
REVERT: A  298 MET cc_start: 0.5956 (tpp) cc_final: 0.5656 (tpt)
REVERT: B   38 ARG cc_start: 0.7272 (mtp-110) cc_final: 0.6927 (mtp85)
REVERT: B   60 ARG cc_start: 0.7037 (ttp80) cc_final: 0.5647 (mmp-170)
REVERT: B  147 ARG cc_start: 0.7487 (ttm-80) cc_final: 0.7040 (pmt170)
REVERT: B  202 ARG cc_start: 0.6972 (mtp85) cc_final: 0.6500 (ptm160)
REVERT: B  261 TYR cc_start: 0.7656 (OUTLIER) cc_final: 0.7327 (m-10)
REVERT: B  280 GLU cc_start: 0.7874 (tp30) cc_final: 0.7277 (tm-30)
REVERT: B  281 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6289 (mp0)
REVERT: B  335 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6639 (tp30)
REVERT: C   52 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7609 (mtp85)
REVERT: C  101 MET cc_start: 0.7652 (OUTLIER) cc_final: 0.7436 (mtp)
REVERT: C  129 ARG cc_start: 0.7363 (mtt180) cc_final: 0.7122 (ttt90)
REVERT: C  188 MET cc_start: 0.7175 (mmm) cc_final: 0.6900 (mmp)
REVERT: C  234 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6844 (m-80)
REVERT: C  269 ILE cc_start: 0.7049 (OUTLIER) cc_final: 0.6564 (mm)
REVERT: H    6 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6263 (pm20)
REVERT: H  235 TYR cc_start: 0.4621 (OUTLIER) cc_final: 0.4199 (t80)
REVERT: H  244 LYS cc_start: 0.8178 (tttt) cc_final: 0.7952 (ttpp)
  outliers start: 44
  outliers final: 27
  residues processed: 152
  average time/residue: 1.3034
  time to fit residues: 211.1595
Evaluate side-chains
  152 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 116
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  199 TYR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  148 ARG
Chi-restraints excluded: chain B residue  183 GLN
Chi-restraints excluded: chain B residue  261 TYR
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  105 TYR
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  138 GLU
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain H residue    6 GLU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  188 LEU
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  235 TYR
Chi-restraints excluded: chain E residue    5 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 65 optimal weight:    0.0570
   chunk 1 optimal weight:    9.9990
   chunk 107 optimal weight:    6.9990
   chunk 51 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0040
   chunk 108 optimal weight:    0.9980
   overall best weight:    0.5510

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

Flipped N/Q/H residues before XYZ refinement:
B 357 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.209630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.167832 restraints weight = 9582.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.4093 rms_B_bonded: 1.97
r_work: 0.3961 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3819 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6927
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9440  Z= 0.170
  Angle     :  0.566   8.180  12799  Z= 0.292
  Chirality :  0.041   0.222   1439
  Planarity :  0.004   0.042   1630
  Dihedral  :  4.837  54.042   1300
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 20.12 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1162
  helix:  2.46 (0.25), residues: 414
  sheet:  0.56 (0.31), residues: 283
  loop : -0.65 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS C 183 
 PHE   0.012   0.001   PHE C 199 
 TYR   0.025   0.001   TYR B 285 
 ARG   0.007   0.000   ARG B 147 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 ILE cc_start: 0.6080 (OUTLIER) cc_final: 0.5732 (tt)
REVERT: A  155 MET cc_start: 0.5882 (ttp) cc_final: 0.5613 (ttm)
REVERT: B   38 ARG cc_start: 0.7180 (mtp-110) cc_final: 0.6831 (mtp85)
REVERT: B   39 GLU cc_start: 0.6418 (tp30) cc_final: 0.6164 (tp30)
REVERT: B   60 ARG cc_start: 0.7044 (ttp80) cc_final: 0.5697 (mmp-170)
REVERT: B  147 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.7113 (pmt170)
REVERT: B  202 ARG cc_start: 0.6981 (mtp85) cc_final: 0.6517 (ptm160)
REVERT: B  280 GLU cc_start: 0.7870 (tp30) cc_final: 0.7233 (tm-30)
REVERT: B  281 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6272 (mp0)
REVERT: B  335 GLU cc_start: 0.6944 (OUTLIER) cc_final: 0.6674 (tp30)
REVERT: C   52 ARG cc_start: 0.7907 (mtt90) cc_final: 0.7623 (mtp85)
REVERT: C  101 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7335 (mtp)
REVERT: C  129 ARG cc_start: 0.7426 (mtt180) cc_final: 0.7161 (ttt90)
REVERT: C  175 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7928 (mm-40)
REVERT: C  188 MET cc_start: 0.7151 (mmm) cc_final: 0.6852 (mmp)
REVERT: C  197 ARG cc_start: 0.7650 (ttt90) cc_final: 0.7416 (tpp-160)
REVERT: C  234 PHE cc_start: 0.7774 (OUTLIER) cc_final: 0.6890 (m-80)
REVERT: D   52 THR cc_start: 0.6048 (t) cc_final: 0.5749 (m)
REVERT: H   67 ARG cc_start: 0.4927 (ptt180) cc_final: 0.4716 (ptt90)
REVERT: H  235 TYR cc_start: 0.4540 (OUTLIER) cc_final: 0.4134 (t80)
REVERT: H  244 LYS cc_start: 0.8163 (tttt) cc_final: 0.7906 (ttpp)
  outliers start: 41
  outliers final: 24
  residues processed: 164
  average time/residue: 1.3837
  time to fit residues: 240.9863
Evaluate side-chains
  149 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 119
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  199 TYR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  148 ARG
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  188 LEU
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  235 TYR
Chi-restraints excluded: chain E residue    5 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 99 optimal weight:    0.0370
   chunk 35 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 110 optimal weight:    2.9990
   chunk 88 optimal weight:    0.0980
   chunk 72 optimal weight:    3.9990
   chunk 107 optimal weight:    9.9990
   chunk 87 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.0264

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 GLN
B 336 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.206127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.169361 restraints weight = 9797.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.4103 rms_B_bonded: 1.76
r_work: 0.3917 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3778 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7006
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9440  Z= 0.228
  Angle     :  0.628  10.792  12799  Z= 0.322
  Chirality :  0.043   0.245   1439
  Planarity :  0.005   0.044   1630
  Dihedral  :  4.838  53.944   1298
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 21.84 %
    Favored  : 74.42 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.25), residues: 1162
  helix:  2.25 (0.25), residues: 413
  sheet:  0.50 (0.31), residues: 283
  loop : -0.71 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C  82 
 HIS   0.004   0.001   HIS C 183 
 PHE   0.033   0.002   PHE A 329 
 TYR   0.025   0.002   TYR H 235 
 ARG   0.006   0.001   ARG B 214 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 ILE cc_start: 0.6132 (OUTLIER) cc_final: 0.5693 (tt)
REVERT: A  155 MET cc_start: 0.5881 (ttp) cc_final: 0.5609 (ttm)
REVERT: A  298 MET cc_start: 0.5833 (tpp) cc_final: 0.5509 (tpt)
REVERT: B   15 ASP cc_start: 0.7470 (m-30) cc_final: 0.7177 (m-30)
REVERT: B   39 GLU cc_start: 0.6386 (tp30) cc_final: 0.6090 (tp30)
REVERT: B   60 ARG cc_start: 0.7122 (ttp80) cc_final: 0.5760 (mmp-170)
REVERT: B  147 ARG cc_start: 0.7566 (ttm-80) cc_final: 0.7183 (pmt170)
REVERT: B  202 ARG cc_start: 0.7115 (mtp85) cc_final: 0.6577 (ptm160)
REVERT: B  280 GLU cc_start: 0.8004 (tp30) cc_final: 0.7363 (tm-30)
REVERT: B  281 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6281 (mp0)
REVERT: B  335 GLU cc_start: 0.7171 (OUTLIER) cc_final: 0.6728 (tp30)
REVERT: C   52 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7627 (mtp85)
REVERT: C  101 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7382 (mtp)
REVERT: C  175 GLN cc_start: 0.8209 (mm-40) cc_final: 0.7988 (mm-40)
REVERT: C  197 ARG cc_start: 0.7731 (ttt90) cc_final: 0.7481 (tpp-160)
REVERT: C  234 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.6908 (m-80)
REVERT: H  235 TYR cc_start: 0.4816 (OUTLIER) cc_final: 0.4380 (t80)
  outliers start: 37
  outliers final: 26
  residues processed: 149
  average time/residue: 1.4157
  time to fit residues: 224.2515
Evaluate side-chains
  146 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  199 TYR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  148 ARG
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  188 LEU
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  235 TYR
Chi-restraints excluded: chain E residue    5 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 74 optimal weight:    0.7980
   chunk 100 optimal weight:    0.4980
   chunk 99 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 59 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 113 optimal weight:    8.9990
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.207175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.170643 restraints weight = 9643.197|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 1.70
r_work: 0.3956 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3820 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9440  Z= 0.189
  Angle     :  0.608   9.001  12799  Z= 0.312
  Chirality :  0.042   0.230   1439
  Planarity :  0.005   0.059   1630
  Dihedral  :  4.770  53.499   1298
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 22.14 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.25), residues: 1162
  helix:  2.27 (0.25), residues: 413
  sheet:  0.55 (0.31), residues: 282
  loop : -0.70 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.004   0.001   HIS C 183 
 PHE   0.013   0.001   PHE C 199 
 TYR   0.027   0.001   TYR B 285 
 ARG   0.013   0.001   ARG B  38 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 118
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: A  116 ILE cc_start: 0.6139 (OUTLIER) cc_final: 0.5730 (tt)
REVERT: A  155 MET cc_start: 0.5914 (ttp) cc_final: 0.5628 (ttm)
REVERT: A  298 MET cc_start: 0.5865 (tpp) cc_final: 0.5504 (tpt)
REVERT: B   38 ARG cc_start: 0.7122 (mtp-110) cc_final: 0.6816 (mtp85)
REVERT: B   39 GLU cc_start: 0.6379 (tp30) cc_final: 0.6110 (tp30)
REVERT: B   60 ARG cc_start: 0.7162 (ttp80) cc_final: 0.5802 (mmp-170)
REVERT: B  147 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7197 (pmt170)
REVERT: B  160 TYR cc_start: 0.5804 (m-10) cc_final: 0.5114 (m-10)
REVERT: B  202 ARG cc_start: 0.7098 (mtp85) cc_final: 0.6602 (ptm160)
REVERT: B  261 TYR cc_start: 0.7706 (OUTLIER) cc_final: 0.6518 (m-80)
REVERT: B  280 GLU cc_start: 0.8039 (tp30) cc_final: 0.7447 (tm-30)
REVERT: B  281 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6242 (mp0)
REVERT: B  335 GLU cc_start: 0.7076 (OUTLIER) cc_final: 0.6676 (tp30)
REVERT: C   52 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7590 (mtp85)
REVERT: C  101 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7368 (mtp)
REVERT: C  175 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7965 (mm-40)
REVERT: C  188 MET cc_start: 0.7168 (mmm) cc_final: 0.6876 (mmp)
REVERT: C  197 ARG cc_start: 0.7748 (ttt90) cc_final: 0.7507 (tpp-160)
REVERT: C  234 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.6926 (m-80)
REVERT: D   52 THR cc_start: 0.6181 (t) cc_final: 0.5837 (m)
REVERT: H  235 TYR cc_start: 0.4631 (OUTLIER) cc_final: 0.4216 (t80)
REVERT: H  244 LYS cc_start: 0.8271 (ttpp) cc_final: 0.7754 (ttpp)
  outliers start: 38
  outliers final: 25
  residues processed: 144
  average time/residue: 1.4022
  time to fit residues: 215.1116
Evaluate side-chains
  148 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  199 TYR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  148 ARG
Chi-restraints excluded: chain B residue  261 TYR
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain C residue  101 MET
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  188 LEU
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  235 TYR
Chi-restraints excluded: chain E residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 48 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9980
   chunk 100 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.206882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.170158 restraints weight = 9714.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.4113 rms_B_bonded: 1.70
r_work: 0.3932 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3796 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9440  Z= 0.217
  Angle     :  0.636  11.426  12799  Z= 0.324
  Chirality :  0.043   0.238   1439
  Planarity :  0.005   0.062   1630
  Dihedral  :  4.829  53.160   1298
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 22.95 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.25), residues: 1162
  helix:  2.14 (0.25), residues: 413
  sheet:  0.54 (0.31), residues: 282
  loop : -0.72 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 332 
 HIS   0.004   0.001   HIS C 183 
 PHE   0.031   0.002   PHE A 329 
 TYR   0.024   0.001   TYR H 235 
 ARG   0.012   0.001   ARG B  38 

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

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

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2324 Ramachandran restraints generated.
    1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 120
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  116 ILE cc_start: 0.6109 (OUTLIER) cc_final: 0.5689 (tt)
REVERT: A  155 MET cc_start: 0.5849 (ttp) cc_final: 0.5572 (ttm)
REVERT: A  298 MET cc_start: 0.5927 (tpp) cc_final: 0.5563 (tpt)
REVERT: B   38 ARG cc_start: 0.7178 (mtp-110) cc_final: 0.6872 (mtp85)
REVERT: B   39 GLU cc_start: 0.6389 (tp30) cc_final: 0.6117 (tp30)
REVERT: B   60 ARG cc_start: 0.7221 (ttp80) cc_final: 0.5829 (mmp-170)
REVERT: B  147 ARG cc_start: 0.7509 (ttm-80) cc_final: 0.7233 (pmt170)
REVERT: B  160 TYR cc_start: 0.5815 (m-10) cc_final: 0.5197 (m-10)
REVERT: B  202 ARG cc_start: 0.7066 (mtp85) cc_final: 0.6599 (ptm160)
REVERT: B  261 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.6464 (m-80)
REVERT: B  280 GLU cc_start: 0.8076 (tp30) cc_final: 0.7454 (tm-30)
REVERT: B  281 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6255 (mp0)
REVERT: B  335 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6634 (tp30)
REVERT: C   52 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7563 (mtp85)
REVERT: C  175 GLN cc_start: 0.8154 (mm-40) cc_final: 0.7924 (mm-40)
REVERT: C  188 MET cc_start: 0.7231 (mmm) cc_final: 0.6959 (mmp)
REVERT: C  197 ARG cc_start: 0.7705 (ttt90) cc_final: 0.7479 (tpp-160)
REVERT: C  234 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.6917 (m-80)
REVERT: C  269 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6997 (mm)
REVERT: D   38 MET cc_start: 0.5567 (ttt) cc_final: 0.5270 (tmt)
REVERT: D   52 THR cc_start: 0.6154 (t) cc_final: 0.5770 (m)
REVERT: H  218 ARG cc_start: 0.6934 (tmm160) cc_final: 0.6695 (tmm160)
REVERT: H  235 TYR cc_start: 0.4756 (OUTLIER) cc_final: 0.4346 (t80)
REVERT: H  244 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7931 (ttpp)
  outliers start: 33
  outliers final: 26
  residues processed: 142
  average time/residue: 1.3635
  time to fit residues: 205.7940
Evaluate side-chains
  150 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 117
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 MET
Chi-restraints excluded: chain A residue  116 ILE
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  199 TYR
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain B residue   10 THR
Chi-restraints excluded: chain B residue   65 SER
Chi-restraints excluded: chain B residue  148 ARG
Chi-restraints excluded: chain B residue  261 TYR
Chi-restraints excluded: chain B residue  281 GLU
Chi-restraints excluded: chain B residue  296 ASP
Chi-restraints excluded: chain B residue  312 MET
Chi-restraints excluded: chain B residue  335 GLU
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  250 CYS
Chi-restraints excluded: chain C residue  263 THR
Chi-restraints excluded: chain C residue  269 ILE
Chi-restraints excluded: chain C residue  270 ILE
Chi-restraints excluded: chain C residue  271 CYS
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  115 THR
Chi-restraints excluded: chain H residue  138 ILE
Chi-restraints excluded: chain H residue  139 VAL
Chi-restraints excluded: chain H residue  172 THR
Chi-restraints excluded: chain H residue  188 LEU
Chi-restraints excluded: chain H residue  215 THR
Chi-restraints excluded: chain H residue  235 TYR
Chi-restraints excluded: chain E residue    5 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 109 optimal weight:    0.6980
   chunk 2 optimal weight:    1.9990
   chunk 108 optimal weight:    0.0570
   chunk 66 optimal weight:    0.5980
   chunk 27 optimal weight:    6.9990
   chunk 100 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
** B  82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.208798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.169965 restraints weight = 9599.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.4112 rms_B_bonded: 2.25
r_work: 0.3947 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3802 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6949
moved from start:          0.4428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9440  Z= 0.176
  Angle     :  0.604   9.083  12799  Z= 0.309
  Chirality :  0.042   0.223   1439
  Planarity :  0.004   0.055   1630
  Dihedral  :  4.767  52.777   1298
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 22.55 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.25), residues: 1162
  helix:  2.27 (0.26), residues: 413
  sheet:  0.62 (0.31), residues: 281
  loop : -0.73 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 332 
 HIS   0.007   0.001   HIS C 183 
 PHE   0.015   0.001   PHE A 329 
 TYR   0.028   0.001   TYR B 285 
 ARG   0.012   0.001   ARG B  38 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12756.87 seconds
wall clock time: 224 minutes 19.38 seconds (13459.38 seconds total)