Starting phenix.real_space_refine
on Tue Mar 11 19:07:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gea_29962/03_2025/8gea_29962.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gea_29962/03_2025/8gea_29962.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gea_29962/03_2025/8gea_29962.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gea_29962/03_2025/8gea_29962.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gea_29962/03_2025/8gea_29962.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gea_29962/03_2025/8gea_29962.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    4221      2.51       5
     N    1140      2.21       5
     O    1148      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6551
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1751
          Classifications: {'peptide': 240}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 66}
          Link IDs: {'PTRANS': 6, 'TRANS': 233}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 249
          Unresolved non-hydrogen angles: 303
          Unresolved non-hydrogen dihedrals: 198
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 6, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 18, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 184
    Chain: "B"
      Number of atoms: 2392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 330, 2392
          Classifications: {'peptide': 330}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 5, 'TRANS': 324}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 146
          Unresolved non-hydrogen angles: 181
          Unresolved non-hydrogen dihedrals: 113
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 10, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 116
    Chain: "G"
      Number of atoms: 335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 335
          Classifications: {'peptide': 50}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 45}
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 65
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "R"
      Number of atoms: 2058
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 282, 2058
          Classifications: {'peptide': 282}
          Incomplete info: {'truncation_to_alanine': 63}
          Link IDs: {'PTRANS': 7, 'TRANS': 274}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 214
          Unresolved non-hydrogen angles: 268
          Unresolved non-hydrogen dihedrals: 170
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 5, 'GLU:plan': 9, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 115
    Chain: "R"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.40, per 1000 atoms: 0.67
  Number of scatterers: 6551
  At special positions: 0
  Unit cell: (68.9, 97.52, 128.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1148      8.00
     N    1140      7.00
     C    4221      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 983.1 milliseconds
  

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1708

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      48.6% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 40
      removed outlier: 3.967A  pdb=" N   GLU A  16 " --> pdb=" O   GLN A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
    Processing helix  chain 'A' and resid 233 through 237
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 303
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 3.642A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 4.418A  pdb=" N   ARG A 317 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.510A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 351 " --> pdb=" O   ARG A 347 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLY A 353 " --> pdb=" O   SER A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 7 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 14 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'R' and resid 31 through 61
      removed outlier: 3.669A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 62 through 65
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 3.777A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 4.702A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
    Processing helix  chain 'R' and resid 137 through 145
      removed outlier: 4.295A  pdb=" N   GLN R 142 " --> pdb=" O   PRO R 138 " (cutoff:3.500A)
      removed outlier: 4.724A  pdb=" N   SER R 143 " --> pdb=" O   PHE R 139 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 146 through 171
      Proline residue:  R 168  - end of helix
      removed outlier: 3.566A  pdb=" N   MET R 171 " --> pdb=" O   LEU R 167 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
    Processing helix  chain 'R' and resid 208 through 237
    Processing helix  chain 'R' and resid 270 through 299
      removed outlier: 3.711A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      Proline residue:  R 288  - end of helix
      removed outlier: 3.879A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 327
      removed outlier: 4.136A  pdb=" N   SER R 319 " --> pdb=" O   GLY R 315 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE R 321 " --> pdb=" O   VAL R 317 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ASN R 322 " --> pdb=" O   ASN R 318 " (cutoff:3.500A)
      Proline residue:  R 323  - end of helix
    Processing helix  chain 'R' and resid 329 through 340
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.597A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   GLY A  47 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.536A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   VAL A 287 " --> pdb=" O   TYR A 360 " (cutoff:3.500A)
      removed outlier: 7.859A  pdb=" N   HIS A 362 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   LEU A 289 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52
      removed outlier: 3.514A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.065A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE B  93 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.533A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.843A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.943A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.793A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.708A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 5.867A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.537A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    390 hydrogen bonds defined for protein.
    1134 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: 1.89

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2117
        1.34 -     1.46: 1403
        1.46 -     1.58: 3114
        1.58 -     1.69: 0
        1.69 -     1.81: 58
  Bond restraints: 6692
  Sorted by residual:
  bond pdb=" CAC G1I R 501 "
       pdb=" CAD G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.448 -0.051 2.00e-02 2.50e+03 6.48e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" CAJ G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.523  1.568 -0.045 2.00e-02 2.50e+03 5.10e+00
  bond pdb=" CAD G1I R 501 "
       pdb=" CAE G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.394  1.438 -0.044 2.00e-02 2.50e+03 4.74e+00
  bond pdb=" CAG G1I R 501 "
       pdb=" CAH G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 2.00e-02 2.50e+03 4.53e+00
  bond pdb=" CAI G1I R 501 "
       pdb=" NAN G1I R 501 "
    ideal  model  delta    sigma   weight residual
    1.451  1.483 -0.032 2.00e-02 2.50e+03 2.59e+00
  ... (remaining 6687 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 8896
        1.17 -     2.34: 195
        2.34 -     3.51: 36
        3.51 -     4.69: 9
        4.69 -     5.86: 9
  Bond angle restraints: 9145
  Sorted by residual:
  angle pdb=" N   GLY A 329 "
        pdb=" CA  GLY A 329 "
        pdb=" C   GLY A 329 "
      ideal   model   delta    sigma   weight residual
     113.18  107.88    5.30 2.37e+00 1.78e-01 5.01e+00
  angle pdb=" CAE G1I R 501 "
        pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
      ideal   model   delta    sigma   weight residual
     112.63  118.49   -5.86 3.00e+00 1.11e-01 3.81e+00
  angle pdb=" C   VAL R 295 "
        pdb=" N   HIS R 296 "
        pdb=" CA  HIS R 296 "
      ideal   model   delta    sigma   weight residual
     120.72  117.50    3.22 1.67e+00 3.59e-01 3.71e+00
  angle pdb=" N   ILE R  55 "
        pdb=" CA  ILE R  55 "
        pdb=" CB  ILE R  55 "
      ideal   model   delta    sigma   weight residual
     110.54  112.95   -2.41 1.36e+00 5.41e-01 3.15e+00
  angle pdb=" CAG G1I R 501 "
        pdb=" CAH G1I R 501 "
        pdb=" CAI G1I R 501 "
      ideal   model   delta    sigma   weight residual
     110.89  116.05   -5.16 3.00e+00 1.11e-01 2.96e+00
  ... (remaining 9140 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 3566
       17.97 -    35.94: 284
       35.94 -    53.91: 23
       53.91 -    71.87: 3
       71.87 -    89.84: 4
  Dihedral angle restraints: 3880
    sinusoidal: 1249
      harmonic: 2631
  Sorted by residual:
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.66   19.34     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CG  ARG A 336 "
           pdb=" CD  ARG A 336 "
           pdb=" NE  ARG A 336 "
           pdb=" CZ  ARG A 336 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.08  -43.08     2      1.50e+01 4.44e-03 9.95e+00
  dihedral pdb=" CA  ALA R  85 "
           pdb=" C   ALA R  85 "
           pdb=" N   VAL R  86 "
           pdb=" CA  VAL R  86 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.76  -15.24     0      5.00e+00 4.00e-02 9.29e+00
  ... (remaining 3877 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 704
       0.030 -    0.061: 264
       0.061 -    0.091: 74
       0.091 -    0.121: 48
       0.121 -    0.151: 5
  Chirality restraints: 1095
  Sorted by residual:
  chirality pdb=" CAJ G1I R 501 "
            pdb=" CAF G1I R 501 "
            pdb=" CAI G1I R 501 "
            pdb=" OAM G1I R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.40    2.55   -0.15 2.00e-01 2.50e+01 5.71e-01
  chirality pdb=" CB  THR A 263 "
            pdb=" CA  THR A 263 "
            pdb=" OG1 THR A 263 "
            pdb=" CG2 THR A 263 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.42    0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE B  58 "
            pdb=" N   ILE B  58 "
            pdb=" C   ILE B  58 "
            pdb=" CB  ILE B  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.11e-01
  ... (remaining 1092 not shown)

  Planarity restraints: 1150
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.010 2.00e-02 2.50e+03   1.05e-02 2.22e+00
        pdb=" CG  TYR B  59 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 193 "   -0.017 5.00e-02 4.00e+02   2.53e-02 1.02e+00
        pdb=" N   PRO B 194 "    0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 194 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 194 "   -0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.016 5.00e-02 4.00e+02   2.50e-02 9.96e-01
        pdb=" N   PRO B 236 "    0.043 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1147 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1600
        2.80 -     3.32: 6354
        3.32 -     3.85: 10867
        3.85 -     4.37: 11896
        4.37 -     4.90: 21791
  Nonbonded interactions: 52508
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 281 "
            pdb=" O   HIS G  44 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   GLY B 310 "
            pdb=" NZ  LYS B 337 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" OE1 GLU R 107 "
            pdb=" OH  TYR R 174 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   PHE G  61 "
     model   vdw
     2.316 3.120
  nonbonded pdb=" OH  TYR R 185 "
            pdb=" O   PHE R 194 "
     model   vdw
     2.327 3.040
  ... (remaining 52503 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.480
  Find NCS groups from input model:        0.070
  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:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
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      :  0.003   0.051   6692  Z= 0.215
  Angle     :  0.476   5.858   9145  Z= 0.255
  Chirality :  0.039   0.151   1095
  Planarity :  0.003   0.025   1150
  Dihedral  : 12.734  89.842   2169
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.28), residues: 888
  helix:  2.33 (0.26), residues: 396
  sheet:  0.02 (0.40), residues: 171
  loop : -0.83 (0.31), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 281 
 HIS   0.005   0.001   HIS A 220 
 PHE   0.010   0.001   PHE R 289 
 TYR   0.026   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B 314 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.831 
Fit side-chains
REVERT: R  277 ILE cc_start: 0.7992 (tt) cc_final: 0.7757 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1710
  time to fit residues: 20.3191
Evaluate side-chains
  68 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 75 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 70 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.140691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.120800 restraints weight = 9916.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.123861 restraints weight = 6116.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.126008 restraints weight = 4390.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.0846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6692  Z= 0.211
  Angle     :  0.478   5.342   9145  Z= 0.266
  Chirality :  0.040   0.178   1095
  Planarity :  0.003   0.026   1150
  Dihedral  :  3.915  30.647    976
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.03 %
    Favored  : 89.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.24 (0.28), residues: 888
  helix:  2.42 (0.26), residues: 400
  sheet: -0.05 (0.39), residues: 174
  loop : -0.78 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.014   0.001   PHE R 289 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.004   0.000   ARG B 219 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.715 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6703 (ttp)
REVERT: R   58 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7863 (mp)
REVERT: R  277 ILE cc_start: 0.7967 (tt) cc_final: 0.7727 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 83
  average time/residue: 0.1628
  time to fit residues: 19.0543
Evaluate side-chains
  77 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  159 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 87 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 83 optimal weight:    0.0020
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  62 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.141290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.120529 restraints weight = 10126.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.123967 restraints weight = 5882.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.126032 restraints weight = 4077.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6692  Z= 0.179
  Angle     :  0.446   5.251   9145  Z= 0.247
  Chirality :  0.040   0.187   1095
  Planarity :  0.003   0.028   1150
  Dihedral  :  3.793  30.487    976
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 12.71 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.28), residues: 888
  helix:  2.53 (0.26), residues: 400
  sheet:  0.08 (0.39), residues: 171
  loop : -0.73 (0.33), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 183 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.017   0.001   TYR B  59 
 ARG   0.004   0.000   ARG B 314 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 75
  time to evaluate  : 0.718 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6832 (ttp)
REVERT: R   58 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7920 (mp)
REVERT: R  277 ILE cc_start: 0.7895 (tt) cc_final: 0.7669 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 80
  average time/residue: 0.1647
  time to fit residues: 19.3569
Evaluate side-chains
  80 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    0.8980
   chunk 47 optimal weight:    0.4980
   chunk 17 optimal weight:    0.2980
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 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 = 0.3787 r_free = 0.3787 target = 0.140909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.120028 restraints weight = 10283.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.123459 restraints weight = 5939.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.125845 restraints weight = 4122.863|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6692  Z= 0.188
  Angle     :  0.441   5.314   9145  Z= 0.244
  Chirality :  0.039   0.148   1095
  Planarity :  0.003   0.027   1150
  Dihedral  :  3.784  31.025    976
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.71 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.28), residues: 888
  helix:  2.49 (0.26), residues: 400
  sheet: -0.02 (0.39), residues: 169
  loop : -0.71 (0.33), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.014   0.001   PHE B 199 
 TYR   0.019   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B 314 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.713 
Fit side-chains
REVERT: R   36 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6796 (ttp)
REVERT: R   58 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7923 (mp)
REVERT: R  277 ILE cc_start: 0.7853 (tt) cc_final: 0.7635 (tp)
  outliers start: 13
  outliers final: 11
  residues processed: 82
  average time/residue: 0.1474
  time to fit residues: 17.5405
Evaluate side-chains
  81 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 23 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 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 = 0.3778 r_free = 0.3778 target = 0.140225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.119398 restraints weight = 10238.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122786 restraints weight = 5927.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.125121 restraints weight = 4132.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6692  Z= 0.197
  Angle     :  0.451   6.823   9145  Z= 0.247
  Chirality :  0.040   0.219   1095
  Planarity :  0.003   0.026   1150
  Dihedral  :  3.778  31.301    976
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.71 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.28), residues: 888
  helix:  2.42 (0.26), residues: 406
  sheet: -0.07 (0.38), residues: 169
  loop : -0.67 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.016   0.001   PHE B 199 
 TYR   0.018   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B 314 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.803 
Fit side-chains
REVERT: B  211 TRP cc_start: 0.9048 (m100) cc_final: 0.8522 (m100)
REVERT: R   36 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6801 (ttp)
REVERT: R   58 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7951 (mp)
  outliers start: 18
  outliers final: 12
  residues processed: 89
  average time/residue: 0.1494
  time to fit residues: 19.3739
Evaluate side-chains
  83 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 46 optimal weight:    0.6980
   chunk 42 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 264 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 = 0.3777 r_free = 0.3777 target = 0.139235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.119357 restraints weight = 10002.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.122475 restraints weight = 6073.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.124623 restraints weight = 4334.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6692  Z= 0.194
  Angle     :  0.451   6.166   9145  Z= 0.247
  Chirality :  0.040   0.225   1095
  Planarity :  0.003   0.026   1150
  Dihedral  :  3.788  31.565    976
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 13.55 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.29), residues: 888
  helix:  2.44 (0.26), residues: 401
  sheet: -0.13 (0.38), residues: 169
  loop : -0.66 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 169 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.015   0.001   PHE B 199 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B 314 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.747 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.7768 (OUTLIER) cc_final: 0.7365 (m-80)
REVERT: B  211 TRP cc_start: 0.9062 (m100) cc_final: 0.8593 (m100)
REVERT: R   36 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6835 (ttp)
REVERT: R   58 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7936 (mp)
  outliers start: 18
  outliers final: 14
  residues processed: 81
  average time/residue: 0.1823
  time to fit residues: 20.9867
Evaluate side-chains
  85 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  159 ILE
Chi-restraints excluded: chain R residue  230 LEU
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 88 optimal weight:    0.0970
   chunk 71 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0570
   chunk 52 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0030
   chunk 36 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.3306

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

Flipped N/Q/H residues before XYZ refinement:
A 264 ASN
** A 292 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 = 0.3812 r_free = 0.3812 target = 0.142125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.122578 restraints weight = 9871.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.125719 restraints weight = 5936.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.127934 restraints weight = 4213.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   6692  Z= 0.125
  Angle     :  0.422   6.362   9145  Z= 0.230
  Chirality :  0.039   0.196   1095
  Planarity :  0.003   0.028   1150
  Dihedral  :  3.664  32.105    976
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 15.22 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.29), residues: 888
  helix:  2.55 (0.26), residues: 405
  sheet: -0.07 (0.38), residues: 169
  loop : -0.65 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP R 313 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 289 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.002   0.000   ARG B 314 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.825 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8397 (mp)
REVERT: B   59 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7217 (m-80)
REVERT: B  211 TRP cc_start: 0.8971 (m100) cc_final: 0.8641 (m100)
REVERT: B  273 ILE cc_start: 0.8771 (mp) cc_final: 0.8501 (mp)
REVERT: R   36 MET cc_start: 0.7426 (OUTLIER) cc_final: 0.7003 (ttp)
REVERT: R   58 ILE cc_start: 0.8303 (OUTLIER) cc_final: 0.7922 (mp)
REVERT: R  277 ILE cc_start: 0.7858 (tt) cc_final: 0.7593 (tp)
  outliers start: 15
  outliers final: 9
  residues processed: 91
  average time/residue: 0.1576
  time to fit residues: 20.5525
Evaluate side-chains
  86 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 7 optimal weight:    0.4980
   chunk 41 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 49 optimal weight:    0.0970
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.5378

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.140912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.121208 restraints weight = 10071.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.124369 restraints weight = 6028.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.126617 restraints weight = 4274.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6692  Z= 0.165
  Angle     :  0.449   6.125   9145  Z= 0.245
  Chirality :  0.040   0.243   1095
  Planarity :  0.003   0.027   1150
  Dihedral  :  3.700  32.851    976
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.89 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.29), residues: 888
  helix:  2.51 (0.26), residues: 405
  sheet: -0.10 (0.38), residues: 169
  loop : -0.67 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 313 
 HIS   0.002   0.001   HIS A 220 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.012   0.001   TYR B  59 
 ARG   0.005   0.000   ARG A 356 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.864 
Fit side-chains
REVERT: B   58 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8432 (mp)
REVERT: B   59 TYR cc_start: 0.7739 (OUTLIER) cc_final: 0.7297 (m-80)
REVERT: B  211 TRP cc_start: 0.9010 (m100) cc_final: 0.8680 (m100)
REVERT: B  273 ILE cc_start: 0.8792 (mp) cc_final: 0.8544 (mp)
REVERT: R   36 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.6872 (ttp)
REVERT: R   58 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7966 (mp)
REVERT: R  277 ILE cc_start: 0.7887 (tt) cc_final: 0.7610 (tp)
  outliers start: 13
  outliers final: 8
  residues processed: 81
  average time/residue: 0.1487
  time to fit residues: 17.7180
Evaluate side-chains
  82 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 70
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0470
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 80 optimal weight:    0.1980
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
** A 292 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 = 0.3809 r_free = 0.3809 target = 0.141901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.122224 restraints weight = 10083.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.125388 restraints weight = 6043.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.127495 restraints weight = 4284.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6692  Z= 0.146
  Angle     :  0.437   5.849   9145  Z= 0.239
  Chirality :  0.040   0.231   1095
  Planarity :  0.003   0.028   1150
  Dihedral  :  3.676  33.003    976
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.89 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.29), residues: 888
  helix:  2.52 (0.26), residues: 405
  sheet: -0.10 (0.38), residues: 174
  loop : -0.65 (0.35), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP R 313 
 HIS   0.002   0.001   HIS A 357 
 PHE   0.012   0.001   PHE R 289 
 TYR   0.011   0.001   TYR R 199 
 ARG   0.004   0.000   ARG A 356 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8705 (p0) cc_final: 0.8492 (p0)
REVERT: B   58 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8408 (mp)
REVERT: B   59 TYR cc_start: 0.7666 (OUTLIER) cc_final: 0.7243 (m-80)
REVERT: B  211 TRP cc_start: 0.8994 (m100) cc_final: 0.8691 (m100)
REVERT: B  273 ILE cc_start: 0.8788 (mp) cc_final: 0.8519 (mp)
REVERT: R   36 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.6899 (ttp)
REVERT: R   58 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7954 (mp)
REVERT: R  277 ILE cc_start: 0.7810 (tt) cc_final: 0.7539 (tp)
  outliers start: 14
  outliers final: 9
  residues processed: 83
  average time/residue: 0.1451
  time to fit residues: 17.6398
Evaluate side-chains
  83 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 79 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.139649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.119682 restraints weight = 10172.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.122831 restraints weight = 6128.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.125025 restraints weight = 4351.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6692  Z= 0.198
  Angle     :  0.459   5.631   9145  Z= 0.252
  Chirality :  0.040   0.226   1095
  Planarity :  0.003   0.027   1150
  Dihedral  :  3.763  34.142    976
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.39 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.29), residues: 888
  helix:  2.48 (0.26), residues: 400
  sheet: -0.26 (0.37), residues: 175
  loop : -0.62 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  63 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.017   0.001   PHE B 199 
 TYR   0.014   0.001   TYR A 253 
 ARG   0.004   0.000   ARG A 356 

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

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

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1776 Ramachandran restraints generated.
    888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.776 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7337 (m-80)
REVERT: B  169 TRP cc_start: 0.9149 (m100) cc_final: 0.8821 (m100)
REVERT: B  211 TRP cc_start: 0.9061 (m100) cc_final: 0.8706 (m100)
REVERT: R   36 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.6835 (ttp)
REVERT: R   58 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7987 (mp)
  outliers start: 13
  outliers final: 9
  residues processed: 79
  average time/residue: 0.1517
  time to fit residues: 17.5372
Evaluate side-chains
  81 residues out of total 781 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.762 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain B residue   58 ILE
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  331 SER
Chi-restraints excluded: chain G residue   41 CYS
Chi-restraints excluded: chain R residue   36 MET
Chi-restraints excluded: chain R residue   58 ILE
Chi-restraints excluded: chain R residue  296 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 16 optimal weight:    4.9990
   overall best weight:    1.0182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.138640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.117637 restraints weight = 10401.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.121044 restraints weight = 6042.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.123387 restraints weight = 4196.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6692  Z= 0.255
  Angle     :  0.490   6.043   9145  Z= 0.268
  Chirality :  0.041   0.227   1095
  Planarity :  0.003   0.027   1150
  Dihedral  :  3.906  34.906    976
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 17.56 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.29), residues: 888
  helix:  2.37 (0.26), residues: 400
  sheet: -0.37 (0.37), residues: 175
  loop : -0.67 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 357 
 PHE   0.020   0.001   PHE B 199 
 TYR   0.016   0.001   TYR A 253 
 ARG   0.003   0.000   ARG A 356 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2105.51 seconds
wall clock time: 37 minutes 18.25 seconds (2238.25 seconds total)