Starting phenix.real_space_refine
on Tue Sep 24 02:39:36 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/09_2024/7sf8_25077_neut.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/09_2024/7sf8_25077.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/09_2024/7sf8_25077.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/09_2024/7sf8_25077.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/09_2024/7sf8_25077_neut.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sf8_25077/09_2024/7sf8_25077_neut.cif"
  }
  resolution = 2.7
  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=   0.015
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      45      5.16       5
     C    4266      2.51       5
     N    1111      2.21       5
     O    1239      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 6661
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1993
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 257, 1993
          Classifications: {'peptide': 257}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 6, 'TRANS': 250}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 52
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 4, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 29
    Chain: "B"
      Number of atoms: 1708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1708
          Classifications: {'peptide': 212}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 3, 'TRANS': 208}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 69
          Unresolved non-hydrogen dihedrals: 50
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 45
    Chain: "C"
      Number of atoms: 2582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2582
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 378
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 378
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 34
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 4.66, per 1000 atoms: 0.70
  Number of scatterers: 6661
  At special positions: 0
  Unit cell: (102.389, 93.7116, 118.007, 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      45     16.00
     O    1239      8.00
     N    1111      7.00
     C    4266      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 469 " - pdb=" SG  CYS A 556 " distance=2.09

  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: 1.52
  Conformation dependent library (CDL) restraints added in 948.8 milliseconds
  

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1624

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      42.3% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.625A  pdb=" N   VAL A 387 " --> pdb=" O   TYR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 427
      removed outlier: 3.640A  pdb=" N   HIS A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR A 402 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 464
      removed outlier: 3.901A  pdb=" N   LYS A 438 " --> pdb=" O   ASP A 434 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A 456 " --> pdb=" O   THR A 452 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   SER A 457 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   GLU A 458 " --> pdb=" O   PHE A 454 " (cutoff:3.500A)
      Proline residue:  A 459  - end of helix
      removed outlier: 3.580A  pdb=" N   LEU A 462 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   THR A 463 " --> pdb=" O   PRO A 459 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLY A 464 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 499
      removed outlier: 4.173A  pdb=" N   ALA A 473 " --> pdb=" O   CYS A 469 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE A 474 " --> pdb=" O   ARG A 470 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   CYS A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   SER A 485 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 529
      removed outlier: 3.585A  pdb=" N   MET A 516 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      Proline residue:  A 521  - end of helix
    Processing helix  chain 'A' and resid 532 through 534
      No H-bonds generated for 'chain 'A' and resid 532 through 534'
    Processing helix  chain 'A' and resid 560 through 568
      removed outlier: 4.043A  pdb=" N   SER A 564 " --> pdb=" O   ASP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 591
    Processing helix  chain 'A' and resid 602 through 614
    Processing helix  chain 'A' and resid 615 through 625
      removed outlier: 4.055A  pdb=" N   PHE A 624 " --> pdb=" O   PHE A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 643
      removed outlier: 3.518A  pdb=" N   VAL A 633 " --> pdb=" O   PHE A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'B' and resid 12 through 26
      removed outlier: 3.579A  pdb=" N   SER B  16 " --> pdb=" O   ALA B  12 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU B  26 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 32
      removed outlier: 3.679A  pdb=" N   VAL B  30 " --> pdb=" O   GLU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 52
    Processing helix  chain 'B' and resid 117 through 130
      removed outlier: 3.607A  pdb=" N   SER B 121 " --> pdb=" O   ARG B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 153
    Processing helix  chain 'B' and resid 157 through 161
    Processing helix  chain 'B' and resid 171 through 185
    Processing helix  chain 'B' and resid 206 through 228
      removed outlier: 3.708A  pdb=" N   ASP B 222 " --> pdb=" O   THR B 218 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLN B 226 " --> pdb=" O   ASP B 222 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 25
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 10 through 24
      removed outlier: 3.540A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 537
    Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 75
      removed outlier: 3.552A  pdb=" N   VAL B  34 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LYS B  35 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   LEU B 107 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   LEU B  37 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   LEU B  39 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.755A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   CYS C 317 " --> pdb=" O   GLY C 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63
      removed outlier: 4.057A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU C  70 " --> pdb=" O   TRP C  82 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.716A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.730A  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: 6.751A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.269A  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: 6.787A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.506A  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: 6.842A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.785A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)

    313 hydrogen bonds defined for protein.
    891 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: 2.95

  Time building geometry restraints manager: 1.78 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: 1784
        1.33 -     1.46: 1405
        1.46 -     1.58: 3538
        1.58 -     1.70: 0
        1.70 -     1.83: 65
  Bond restraints: 6792
  Sorted by residual:
  bond pdb=" CA  SER A 465 "
       pdb=" CB  SER A 465 "
    ideal  model  delta    sigma   weight residual
    1.530  1.454  0.076 1.43e-02 4.89e+03 2.80e+01
  bond pdb=" CA  SER A 564 "
       pdb=" CB  SER A 564 "
    ideal  model  delta    sigma   weight residual
    1.529  1.463  0.066 1.55e-02 4.16e+03 1.83e+01
  bond pdb=" CA  SER A 472 "
       pdb=" CB  SER A 472 "
    ideal  model  delta    sigma   weight residual
    1.528  1.461  0.067 1.59e-02 3.96e+03 1.78e+01
  bond pdb=" CA  SER A 561 "
       pdb=" CB  SER A 561 "
    ideal  model  delta    sigma   weight residual
    1.531  1.468  0.063 1.56e-02 4.11e+03 1.63e+01
  bond pdb=" N   ILE A 558 "
       pdb=" CA  ILE A 558 "
    ideal  model  delta    sigma   weight residual
    1.458  1.506 -0.048 1.20e-02 6.94e+03 1.57e+01
  ... (remaining 6787 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.41: 8692
        1.41 -     2.81: 389
        2.81 -     4.22: 110
        4.22 -     5.63: 19
        5.63 -     7.04: 6
  Bond angle restraints: 9216
  Sorted by residual:
  angle pdb=" N   ARG A 470 "
        pdb=" CA  ARG A 470 "
        pdb=" C   ARG A 470 "
      ideal   model   delta    sigma   weight residual
     113.50  106.46    7.04 1.23e+00 6.61e-01 3.27e+01
  angle pdb=" N   GLN B 226 "
        pdb=" CA  GLN B 226 "
        pdb=" C   GLN B 226 "
      ideal   model   delta    sigma   weight residual
     113.12  106.97    6.15 1.25e+00 6.40e-01 2.42e+01
  angle pdb=" N   LEU A 481 "
        pdb=" CA  LEU A 481 "
        pdb=" C   LEU A 481 "
      ideal   model   delta    sigma   weight residual
     113.18  107.56    5.62 1.21e+00 6.83e-01 2.16e+01
  angle pdb=" N   ALA A 467 "
        pdb=" CA  ALA A 467 "
        pdb=" CB  ALA A 467 "
      ideal   model   delta    sigma   weight residual
     110.59  105.33    5.26 1.33e+00 5.65e-01 1.57e+01
  angle pdb=" N   MET A 655 "
        pdb=" CA  MET A 655 "
        pdb=" C   MET A 655 "
      ideal   model   delta    sigma   weight residual
     111.36  107.22    4.14 1.09e+00 8.42e-01 1.44e+01
  ... (remaining 9211 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.21: 3644
       17.21 -    34.43: 307
       34.43 -    51.64: 51
       51.64 -    68.85: 5
       68.85 -    86.06: 4
  Dihedral angle restraints: 4011
    sinusoidal: 1508
      harmonic: 2503
  Sorted by residual:
  dihedral pdb=" CA  ASP C 258 "
           pdb=" C   ASP C 258 "
           pdb=" N   GLN C 259 "
           pdb=" CA  GLN C 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.32   20.68     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  VAL A 531 "
           pdb=" C   VAL A 531 "
           pdb=" N   ASP A 532 "
           pdb=" CA  ASP A 532 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.53   20.47     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  ARG A 429 "
           pdb=" C   ARG A 429 "
           pdb=" N   ARG A 430 "
           pdb=" CA  ARG A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.54  -18.46     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 4008 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 860
       0.056 -    0.113: 174
       0.113 -    0.169: 38
       0.169 -    0.226: 5
       0.226 -    0.282: 2
  Chirality restraints: 1079
  Sorted by residual:
  chirality pdb=" CA  TYR A 536 "
            pdb=" N   TYR A 536 "
            pdb=" C   TYR A 536 "
            pdb=" CB  TYR A 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.99e+00
  chirality pdb=" CA  ILE A 540 "
            pdb=" N   ILE A 540 "
            pdb=" C   ILE A 540 "
            pdb=" CB  ILE A 540 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  ARG A 470 "
            pdb=" N   ARG A 470 "
            pdb=" C   ARG A 470 "
            pdb=" CB  ARG A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1076 not shown)

  Planarity restraints: 1160
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 469 "    0.015 2.00e-02 2.50e+03   3.05e-02 9.28e+00
        pdb=" C   CYS A 469 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   CYS A 469 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG A 470 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 558 "   -0.012 2.00e-02 2.50e+03   2.51e-02 6.32e+00
        pdb=" C   ILE A 558 "    0.043 2.00e-02 2.50e+03
        pdb=" O   ILE A 558 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ARG A 559 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 557 "    0.011 2.00e-02 2.50e+03   2.20e-02 4.82e+00
        pdb=" C   TRP A 557 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   TRP A 557 "    0.014 2.00e-02 2.50e+03
        pdb=" N   ILE A 558 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1157 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1607
        2.80 -     3.32: 5912
        3.32 -     3.85: 10104
        3.85 -     4.37: 12052
        4.37 -     4.90: 21621
  Nonbonded interactions: 51296
  Sorted by model distance:
  nonbonded pdb=" NE1 TRP A 617 "
            pdb=" OE1 GLN A 644 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" O   TYR A 505 "
            pdb=" NH2 ARG B  32 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" O   GLY B  40 "
            pdb=" NH2 ARG B  90 "
     model   vdw
     2.371 3.120
  nonbonded pdb=" O   VAL A 563 "
            pdb=" OG1 THR A 567 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" O   ASP C 228 "
            pdb=" OG  SER C 245 "
     model   vdw
     2.397 3.040
  ... (remaining 51291 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.800
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.240
  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:16.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
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      :  0.005   0.076   6792  Z= 0.347
  Angle     :  0.740   7.037   9216  Z= 0.475
  Chirality :  0.050   0.282   1079
  Planarity :  0.004   0.054   1160
  Dihedral  : 13.034  86.064   2384
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.97 %
    Favored  : 98.89 %
  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:  0.40 (0.30), residues: 846
  helix:  1.57 (0.30), residues: 341
  sheet:  0.81 (0.41), residues: 161
  loop : -1.40 (0.31), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  82 
 HIS   0.004   0.001   HIS B 221 
 PHE   0.021   0.002   PHE A 649 
 TYR   0.014   0.002   TYR A 408 
 ARG   0.006   0.000   ARG A 559 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.740 
Fit side-chains
REVERT: A  506 VAL cc_start: 0.8055 (t) cc_final: 0.7849 (t)
REVERT: A  520 PHE cc_start: 0.7693 (t80) cc_final: 0.7443 (t80)
REVERT: A  580 MET cc_start: 0.8415 (mmm) cc_final: 0.8156 (mmt)
REVERT: A  590 ILE cc_start: 0.8046 (mm) cc_final: 0.7796 (mp)
REVERT: B   89 GLN cc_start: 0.6281 (mp-120) cc_final: 0.6060 (mp-120)
REVERT: B  147 ASP cc_start: 0.7144 (p0) cc_final: 0.6789 (p0)
REVERT: B  151 GLU cc_start: 0.7436 (mp0) cc_final: 0.6841 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 141
  average time/residue: 1.2782
  time to fit residues: 188.5719
Evaluate side-chains
  120 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  559 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0470
   chunk 34 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.1845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6792  Z= 0.260
  Angle     :  0.551   5.642   9216  Z= 0.298
  Chirality :  0.043   0.137   1079
  Planarity :  0.004   0.054   1160
  Dihedral  :  4.544  51.362    919
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 10.43 %
    Favored  : 88.18 %
  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:  0.74 (0.30), residues: 846
  helix:  1.85 (0.30), residues: 349
  sheet:  1.02 (0.40), residues: 171
  loop : -1.37 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 486 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.023   0.002   PHE A 649 
 TYR   0.011   0.001   TYR A 408 
 ARG   0.004   0.000   ARG A 496 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.737 
Fit side-chains
REVERT: A  555 MET cc_start: 0.7184 (tmm) cc_final: 0.6875 (ttp)
REVERT: A  580 MET cc_start: 0.8320 (mmm) cc_final: 0.8035 (mmt)
REVERT: A  590 ILE cc_start: 0.8158 (mm) cc_final: 0.7933 (mp)
REVERT: B   20 ASP cc_start: 0.8190 (m-30) cc_final: 0.7794 (m-30)
REVERT: B  151 GLU cc_start: 0.7433 (mp0) cc_final: 0.6951 (mp0)
REVERT: C  164 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8357 (m)
  outliers start: 10
  outliers final: 2
  residues processed: 135
  average time/residue: 1.1524
  time to fit residues: 163.4447
Evaluate side-chains
  111 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 108
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain C residue  164 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 63 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0870
   chunk 76 optimal weight:    0.0970
   chunk 82 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 75 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6792  Z= 0.234
  Angle     :  0.518   6.083   9216  Z= 0.281
  Chirality :  0.042   0.136   1079
  Planarity :  0.003   0.052   1160
  Dihedral  :  4.108  17.323    915
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 12.52 %
    Favored  : 85.54 %
  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:  0.85 (0.30), residues: 846
  helix:  1.98 (0.30), residues: 350
  sheet:  1.04 (0.40), residues: 173
  loop : -1.37 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  82 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.023   0.001   PHE A 649 
 TYR   0.011   0.001   TYR A 408 
 ARG   0.002   0.000   ARG C 219 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 120
  time to evaluate  : 0.709 
Fit side-chains
REVERT: A  555 MET cc_start: 0.7006 (OUTLIER) cc_final: 0.6665 (ttt)
REVERT: A  580 MET cc_start: 0.8259 (mmm) cc_final: 0.7963 (mmt)
REVERT: A  590 ILE cc_start: 0.8212 (mm) cc_final: 0.7978 (mp)
REVERT: A  646 PHE cc_start: 0.7688 (t80) cc_final: 0.7173 (t80)
REVERT: B   20 ASP cc_start: 0.8189 (m-30) cc_final: 0.7745 (m-30)
REVERT: B  213 ARG cc_start: 0.6576 (mtt90) cc_final: 0.6137 (mtt90)
REVERT: C  164 THR cc_start: 0.8737 (OUTLIER) cc_final: 0.8365 (m)
  outliers start: 14
  outliers final: 7
  residues processed: 124
  average time/residue: 1.3240
  time to fit residues: 172.2122
Evaluate side-chains
  125 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue  164 GLU
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  228 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 51 optimal weight:    0.1980
   chunk 76 optimal weight:    0.3980
   chunk 81 optimal weight:    0.4980
   chunk 40 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 175 GLN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6792  Z= 0.214
  Angle     :  0.506   6.835   9216  Z= 0.272
  Chirality :  0.042   0.134   1079
  Planarity :  0.003   0.050   1160
  Dihedral  :  4.016  17.969    915
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.21 %
    Favored  : 84.56 %
  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:  0.94 (0.31), residues: 846
  helix:  2.10 (0.30), residues: 350
  sheet:  1.03 (0.40), residues: 173
  loop : -1.34 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  82 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.022   0.001   PHE A 649 
 TYR   0.009   0.001   TYR A 408 
 ARG   0.003   0.000   ARG C 134 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A  555 MET cc_start: 0.6929 (OUTLIER) cc_final: 0.6669 (ttt)
REVERT: A  580 MET cc_start: 0.8234 (mmm) cc_final: 0.7986 (mmm)
REVERT: A  646 PHE cc_start: 0.7639 (t80) cc_final: 0.7117 (t80)
REVERT: B   20 ASP cc_start: 0.8181 (m-30) cc_final: 0.7725 (m-30)
REVERT: B  181 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7079 (mm-30)
REVERT: C   20 ASP cc_start: 0.7244 (m-30) cc_final: 0.6983 (m-30)
REVERT: C  164 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8354 (m)
  outliers start: 16
  outliers final: 10
  residues processed: 127
  average time/residue: 1.2794
  time to fit residues: 170.8396
Evaluate side-chains
  127 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue  164 GLU
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  228 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 0 optimal weight:    0.8980
   chunk 41 optimal weight:    0.2980
   chunk 72 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 259 GLN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6792  Z= 0.306
  Angle     :  0.556   7.636   9216  Z= 0.296
  Chirality :  0.044   0.139   1079
  Planarity :  0.004   0.052   1160
  Dihedral  :  4.183  19.120    915
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.60 %
    Favored  : 83.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.30), residues: 846
  helix:  2.07 (0.30), residues: 350
  sheet:  0.94 (0.40), residues: 173
  loop : -1.33 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  82 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.026   0.002   PHE A 649 
 TYR   0.025   0.002   TYR A 495 
 ARG   0.004   0.000   ARG C 134 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.739 
Fit side-chains
REVERT: A  555 MET cc_start: 0.6889 (OUTLIER) cc_final: 0.6523 (ttp)
REVERT: A  580 MET cc_start: 0.8233 (mmm) cc_final: 0.7996 (mmt)
REVERT: B   20 ASP cc_start: 0.8185 (m-30) cc_final: 0.7743 (m-30)
REVERT: B   89 GLN cc_start: 0.6608 (mp-120) cc_final: 0.6335 (mp-120)
REVERT: B  151 GLU cc_start: 0.7455 (mp0) cc_final: 0.7061 (mp0)
REVERT: B  181 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7049 (mm-30)
REVERT: C   20 ASP cc_start: 0.7271 (m-30) cc_final: 0.6999 (m-30)
REVERT: C  164 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8486 (m)
  outliers start: 16
  outliers final: 12
  residues processed: 128
  average time/residue: 1.2341
  time to fit residues: 166.1136
Evaluate side-chains
  129 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 115
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue  164 GLU
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  228 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 73 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 175 GLN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057   6792  Z= 0.369
  Angle     :  0.592   7.288   9216  Z= 0.315
  Chirality :  0.045   0.145   1079
  Planarity :  0.004   0.054   1160
  Dihedral  :  4.331  22.730    915
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 15.02 %
    Favored  : 81.92 %
  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:  0.81 (0.30), residues: 846
  helix:  2.01 (0.30), residues: 349
  sheet:  0.97 (0.41), residues: 166
  loop : -1.38 (0.32), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  82 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.028   0.002   PHE A 649 
 TYR   0.021   0.002   TYR A 495 
 ARG   0.004   0.000   ARG C 134 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A  555 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6689 (ttt)
REVERT: A  580 MET cc_start: 0.8214 (mmm) cc_final: 0.8007 (mmm)
REVERT: B   89 GLN cc_start: 0.6630 (mp-120) cc_final: 0.6356 (mp-120)
REVERT: B  151 GLU cc_start: 0.7479 (mp0) cc_final: 0.7040 (mp0)
REVERT: B  181 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7039 (mm-30)
REVERT: C   44 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7578 (mt0)
REVERT: C  164 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8562 (m)
  outliers start: 22
  outliers final: 15
  residues processed: 128
  average time/residue: 1.3052
  time to fit residues: 175.1529
Evaluate side-chains
  126 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain B residue  164 GLU
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   44 GLN
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  323 ASP
Chi-restraints excluded: chain C residue  336 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0060
   chunk 59 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 37 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.6196

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 268 ASN
C 293 ASN
D  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6792  Z= 0.277
  Angle     :  0.550   6.978   9216  Z= 0.294
  Chirality :  0.043   0.134   1079
  Planarity :  0.003   0.052   1160
  Dihedral  :  4.248  25.866    915
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.58 %
    Favored  : 81.92 %
  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:  0.92 (0.30), residues: 846
  helix:  2.23 (0.30), residues: 343
  sheet:  0.91 (0.41), residues: 168
  loop : -1.35 (0.32), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  82 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.024   0.002   PHE A 649 
 TYR   0.018   0.001   TYR A 495 
 ARG   0.005   0.000   ARG C 134 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  555 MET cc_start: 0.6883 (OUTLIER) cc_final: 0.6668 (ttt)
REVERT: A  580 MET cc_start: 0.8196 (mmm) cc_final: 0.7988 (mmt)
REVERT: B   89 GLN cc_start: 0.6593 (mp-120) cc_final: 0.6291 (mp-120)
REVERT: B  151 GLU cc_start: 0.7463 (mp0) cc_final: 0.7026 (mp0)
REVERT: B  181 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7044 (mm-30)
REVERT: C   44 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7604 (mt0)
REVERT: C  164 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8509 (m)
  outliers start: 18
  outliers final: 15
  residues processed: 117
  average time/residue: 1.3762
  time to fit residues: 168.3892
Evaluate side-chains
  131 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue  164 GLU
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   44 GLN
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  336 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0770
   chunk 63 optimal weight:    0.0040
   chunk 73 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.4150

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 175 GLN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6792  Z= 0.201
  Angle     :  0.509   6.409   9216  Z= 0.272
  Chirality :  0.042   0.129   1079
  Planarity :  0.003   0.050   1160
  Dihedral  :  4.027  28.544    915
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.11 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.12 (0.30), residues: 846
  helix:  2.52 (0.30), residues: 339
  sheet:  0.98 (0.41), residues: 169
  loop : -1.34 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.022   0.001   PHE A 649 
 TYR   0.025   0.001   TYR A 495 
 ARG   0.006   0.000   ARG C 134 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A  580 MET cc_start: 0.8186 (mmm) cc_final: 0.7984 (mmt)
REVERT: B   20 ASP cc_start: 0.8125 (m-30) cc_final: 0.7659 (m-30)
REVERT: B   89 GLN cc_start: 0.6550 (mp-120) cc_final: 0.6250 (mp-120)
REVERT: B  151 GLU cc_start: 0.7449 (mp0) cc_final: 0.7077 (mp0)
REVERT: B  181 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7062 (mm-30)
REVERT: C  164 THR cc_start: 0.8716 (OUTLIER) cc_final: 0.8373 (m)
  outliers start: 17
  outliers final: 11
  residues processed: 126
  average time/residue: 1.2373
  time to fit residues: 163.8842
Evaluate side-chains
  120 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.730 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain B residue  164 GLU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  336 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:    0.4980
   chunk 68 optimal weight:    1.9990
   chunk 71 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 268 ASN
C 293 ASN
C 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.3155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6792  Z= 0.308
  Angle     :  0.558   6.922   9216  Z= 0.298
  Chirality :  0.044   0.138   1079
  Planarity :  0.004   0.052   1160
  Dihedral  :  4.143  25.420    915
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.11 %
    Favored  : 80.95 %
  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:  1.00 (0.30), residues: 846
  helix:  2.31 (0.30), residues: 341
  sheet:  0.95 (0.41), residues: 168
  loop : -1.30 (0.32), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  82 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.025   0.002   PHE A 649 
 TYR   0.029   0.002   TYR A 495 
 ARG   0.005   0.000   ARG C 134 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.737 
Fit side-chains
REVERT: B   89 GLN cc_start: 0.6625 (mp-120) cc_final: 0.6320 (mp-120)
REVERT: B  147 ASP cc_start: 0.7485 (p0) cc_final: 0.7230 (p0)
REVERT: B  151 GLU cc_start: 0.7464 (mp0) cc_final: 0.7019 (mp0)
REVERT: B  181 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7076 (mm-30)
REVERT: C   44 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.7737 (mt0)
REVERT: C  164 THR cc_start: 0.8811 (OUTLIER) cc_final: 0.8485 (m)
  outliers start: 14
  outliers final: 11
  residues processed: 120
  average time/residue: 1.2892
  time to fit residues: 162.0501
Evaluate side-chains
  123 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain B residue  164 GLU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   44 GLN
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 55 optimal weight:    0.9990
   chunk 83 optimal weight:    0.0670
   chunk 77 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 6 optimal weight:    0.3980
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   chunk 70 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 268 ASN
C 293 ASN
C 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6792  Z= 0.236
  Angle     :  0.527   6.262   9216  Z= 0.281
  Chirality :  0.042   0.131   1079
  Planarity :  0.003   0.051   1160
  Dihedral  :  3.988  19.253    915
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.80 %
    Favored  : 80.39 %
  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:  1.10 (0.30), residues: 846
  helix:  2.51 (0.30), residues: 337
  sheet:  0.99 (0.40), residues: 169
  loop : -1.34 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.023   0.001   PHE A 649 
 TYR   0.027   0.001   TYR A 495 
 ARG   0.005   0.000   ARG C 134 

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.828 
Fit side-chains
REVERT: B   89 GLN cc_start: 0.6585 (mp-120) cc_final: 0.6283 (mp-120)
REVERT: B  147 ASP cc_start: 0.7462 (p0) cc_final: 0.7215 (p0)
REVERT: B  151 GLU cc_start: 0.7438 (mp0) cc_final: 0.6997 (mp0)
REVERT: B  181 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7076 (mm-30)
REVERT: C  164 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8444 (m)
  outliers start: 13
  outliers final: 11
  residues processed: 118
  average time/residue: 1.3729
  time to fit residues: 169.5806
Evaluate side-chains
  121 residues out of total 748 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.843 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  633 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain B residue  164 GLU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    0.4980
   chunk 66 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.123249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.104164 restraints weight = 9639.335|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.83
r_work: 0.3345 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6792  Z= 0.292
  Angle     :  0.558   6.716   9216  Z= 0.297
  Chirality :  0.044   0.136   1079
  Planarity :  0.003   0.052   1160
  Dihedral  :  4.056  17.001    915
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 18.36 %
    Favored  : 79.83 %
  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:  0.95 (0.30), residues: 846
  helix:  2.22 (0.30), residues: 348
  sheet:  0.97 (0.40), residues: 169
  loop : -1.39 (0.31), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  82 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.024   0.002   PHE A 649 
 TYR   0.028   0.002   TYR A 495 
 ARG   0.005   0.000   ARG C 134 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3309.06 seconds
wall clock time: 61 minutes 38.25 seconds (3698.25 seconds total)