Starting phenix.real_space_refine
on Thu Jul 24 21:22:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sf8_25077/07_2025/7sf8_25077_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sf8_25077/07_2025/7sf8_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/cci-nas-00/data/ceres_data/7sf8_25077/07_2025/7sf8_25077.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sf8_25077/07_2025/7sf8_25077.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sf8_25077/07_2025/7sf8_25077_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sf8_25077/07_2025/7sf8_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-5711/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: 5.40, per 1000 atoms: 0.81
  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: 1.91
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 0.87
  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: 4.71

  Time building geometry restraints manager: 2.06 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:             3.050
  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:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     25.730
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.100
  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:             0.020
  Load rotamer database and sin/cos tables:25.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   55.120
-------------------------------------------------------------------------------
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      :  0.006   0.076   6793  Z= 0.317
  Angle     :  0.749  11.134   9218  Z= 0.478
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20343 (  313)
  hydrogen bonds       : angle       5.67558 (  891)
  SS BOND              : bond        0.05606 (    1)
  SS BOND              : angle       7.87390 (    2)
  covalent geometry    : bond        0.00547 ( 6792)
  covalent geometry    : angle       0.73982 ( 9216)

*********************** 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 to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 2.529 
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: 2.4186
  time to fit residues: 360.7602
Evaluate side-chains
  120 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
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:    0.0070
   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:    0.3896

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.130147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.110641 restraints weight = 9780.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.87
r_work: 0.3415 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6793  Z= 0.145
  Angle     :  0.526   5.292   9218  Z= 0.284
  Chirality :  0.042   0.138   1079
  Planarity :  0.004   0.052   1160
  Dihedral  :  4.435  48.841    919
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  9.60 %
    Favored  : 88.73 %
  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:  0.80 (0.30), residues: 846
  helix:  1.90 (0.30), residues: 349
  sheet:  1.07 (0.41), residues: 171
  loop : -1.35 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 486 
 HIS   0.006   0.001   HIS A 401 
 PHE   0.021   0.002   PHE A 649 
 TYR   0.010   0.001   TYR A 408 
 ARG   0.005   0.000   ARG A 496 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05683 (  313)
  hydrogen bonds       : angle       4.10795 (  891)
  SS BOND              : bond        0.00542 (    1)
  SS BOND              : angle       1.62933 (    2)
  covalent geometry    : bond        0.00324 ( 6792)
  covalent geometry    : angle       0.52529 ( 9216)

*********************** 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
  145 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 0.827 
Fit side-chains
REVERT: A  555 MET cc_start: 0.7475 (tmm) cc_final: 0.7209 (ttp)
REVERT: A  562 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7645 (tp)
REVERT: A  629 PHE cc_start: 0.8070 (t80) cc_final: 0.7540 (t80)
REVERT: B   20 ASP cc_start: 0.8453 (m-30) cc_final: 0.8083 (m-30)
REVERT: B   52 GLN cc_start: 0.7591 (mt0) cc_final: 0.7334 (tt0)
REVERT: B   89 GLN cc_start: 0.6527 (mp-120) cc_final: 0.6314 (mp-120)
REVERT: C  164 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8397 (m)
  outliers start: 12
  outliers final: 2
  residues processed: 137
  average time/residue: 1.2825
  time to fit residues: 185.5925
Evaluate side-chains
  112 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  562 LEU
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 26 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 19 optimal weight:    0.1980
   chunk 43 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C 175 GLN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.126325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.106758 restraints weight = 9764.442|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.85
r_work: 0.3353 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6793  Z= 0.183
  Angle     :  0.542   7.865   9218  Z= 0.291
  Chirality :  0.043   0.139   1079
  Planarity :  0.004   0.052   1160
  Dihedral  :  4.154  17.404    915
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.52 %
    Favored  : 85.40 %
  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:  0.82 (0.30), residues: 846
  helix:  1.93 (0.30), residues: 350
  sheet:  1.02 (0.40), residues: 173
  loop : -1.34 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  82 
 HIS   0.006   0.001   HIS B 221 
 PHE   0.025   0.002   PHE A 649 
 TYR   0.009   0.001   TYR A 408 
 ARG   0.004   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06496 (  313)
  hydrogen bonds       : angle       4.11966 (  891)
  SS BOND              : bond        0.00442 (    1)
  SS BOND              : angle       1.65530 (    2)
  covalent geometry    : bond        0.00431 ( 6792)
  covalent geometry    : angle       0.54176 ( 9216)

*********************** 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
  135 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 120
  time to evaluate  : 0.802 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7669 (ttp-170)
REVERT: A  555 MET cc_start: 0.7482 (tmm) cc_final: 0.7186 (ttt)
REVERT: A  629 PHE cc_start: 0.8095 (t80) cc_final: 0.7567 (t80)
REVERT: B   20 ASP cc_start: 0.8445 (m-30) cc_final: 0.8019 (m-30)
REVERT: B   52 GLN cc_start: 0.7588 (mt0) cc_final: 0.7291 (tt0)
REVERT: B   89 GLN cc_start: 0.6637 (mp-120) cc_final: 0.6340 (mp-120)
REVERT: B  209 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7056 (mtm110)
REVERT: C   40 VAL cc_start: 0.8842 (t) cc_final: 0.8621 (m)
REVERT: C  164 THR cc_start: 0.8812 (OUTLIER) cc_final: 0.8454 (m)
  outliers start: 15
  outliers final: 9
  residues processed: 124
  average time/residue: 1.3248
  time to fit residues: 172.6597
Evaluate side-chains
  128 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.736 
-------------------------------------------------------------------------------
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  496 ARG
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  562 LEU
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  209 ARG
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 12 optimal weight:    0.0270
   chunk 23 optimal weight:    0.9980
   chunk 79 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0970
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
C 175 GLN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.127463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.108112 restraints weight = 9811.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.86
r_work: 0.3373 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6793  Z= 0.142
  Angle     :  0.497   6.849   9218  Z= 0.266
  Chirality :  0.042   0.134   1079
  Planarity :  0.003   0.050   1160
  Dihedral  :  3.999  18.730    915
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 13.49 %
    Favored  : 83.73 %
  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:  1.03 (0.30), residues: 846
  helix:  2.29 (0.30), residues: 339
  sheet:  1.01 (0.40), residues: 173
  loop : -1.26 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   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   0.002   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05543 (  313)
  hydrogen bonds       : angle       3.94002 (  891)
  SS BOND              : bond        0.00375 (    1)
  SS BOND              : angle       1.16143 (    2)
  covalent geometry    : bond        0.00327 ( 6792)
  covalent geometry    : angle       0.49674 ( 9216)

*********************** 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
  144 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  495 TYR cc_start: 0.8310 (t80) cc_final: 0.8063 (t80)
REVERT: A  496 ARG cc_start: 0.8054 (ttt-90) cc_final: 0.7737 (ttp-170)
REVERT: A  555 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7025 (ttt)
REVERT: B   20 ASP cc_start: 0.8443 (m-30) cc_final: 0.8002 (m-30)
REVERT: B   52 GLN cc_start: 0.7551 (mt0) cc_final: 0.7274 (tt0)
REVERT: B   89 GLN cc_start: 0.6644 (mp-120) cc_final: 0.6270 (mp-120)
REVERT: B  181 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7643 (mm-30)
REVERT: C   20 ASP cc_start: 0.7334 (m-30) cc_final: 0.7082 (m-30)
REVERT: C  164 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8421 (m)
  outliers start: 20
  outliers final: 11
  residues processed: 132
  average time/residue: 1.2342
  time to fit residues: 171.4226
Evaluate side-chains
  132 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  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  506 VAL
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  562 LEU
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  164 THR
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  323 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 74 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 22 optimal weight:    0.2980
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0770
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
C 259 GLN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.126501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.107044 restraints weight = 9819.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 1.86
r_work: 0.3357 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3229 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6793  Z= 0.157
  Angle     :  0.509   7.013   9218  Z= 0.272
  Chirality :  0.042   0.137   1079
  Planarity :  0.003   0.050   1160
  Dihedral  :  4.006  20.533    915
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.30 %
    Favored  : 82.20 %
  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:  2.39 (0.30), residues: 339
  sheet:  1.00 (0.40), residues: 173
  loop : -1.25 (0.33), residues: 334

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   0.025   0.002   PHE A 629 
 TYR   0.009   0.001   TYR A 408 
 ARG   0.004   0.000   ARG C  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05833 (  313)
  hydrogen bonds       : angle       3.96158 (  891)
  SS BOND              : bond        0.00428 (    1)
  SS BOND              : angle       1.29105 (    2)
  covalent geometry    : bond        0.00368 ( 6792)
  covalent geometry    : angle       0.50869 ( 9216)

*********************** 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
  141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 123
  time to evaluate  : 0.735 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7722 (ttp-170)
REVERT: A  555 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7010 (ttp)
REVERT: A  629 PHE cc_start: 0.8156 (t80) cc_final: 0.7742 (t80)
REVERT: A  646 PHE cc_start: 0.8004 (t80) cc_final: 0.7454 (t80)
REVERT: B   20 ASP cc_start: 0.8441 (m-30) cc_final: 0.8000 (m-30)
REVERT: B   52 GLN cc_start: 0.7563 (mt0) cc_final: 0.7277 (tt0)
REVERT: B   89 GLN cc_start: 0.6665 (mp-120) cc_final: 0.6244 (mp-120)
REVERT: B   98 GLU cc_start: 0.5928 (mm-30) cc_final: 0.5654 (mm-30)
REVERT: B  181 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7618 (mm-30)
REVERT: C   20 ASP cc_start: 0.7359 (m-30) cc_final: 0.7104 (m-30)
REVERT: C  164 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8461 (m)
  outliers start: 18
  outliers final: 11
  residues processed: 129
  average time/residue: 1.2746
  time to fit residues: 172.5349
Evaluate side-chains
  133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
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  496 ARG
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  562 LEU
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 35 optimal weight:    0.4980
   chunk 5 optimal weight:    0.4980
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 21 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    0.4980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.126223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.106758 restraints weight = 9718.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.86
r_work: 0.3353 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6793  Z= 0.172
  Angle     :  0.528   6.459   9218  Z= 0.282
  Chirality :  0.043   0.134   1079
  Planarity :  0.004   0.050   1160
  Dihedral  :  4.069  23.616    915
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 14.46 %
    Favored  : 82.48 %
  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:  2.45 (0.30), residues: 338
  sheet:  0.99 (0.40), residues: 173
  loop : -1.27 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.024   0.002   PHE A 649 
 TYR   0.009   0.001   TYR A 408 
 ARG   0.009   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06129 (  313)
  hydrogen bonds       : angle       4.00412 (  891)
  SS BOND              : bond        0.00480 (    1)
  SS BOND              : angle       1.37190 (    2)
  covalent geometry    : bond        0.00410 ( 6792)
  covalent geometry    : angle       0.52736 ( 9216)

*********************** 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
  141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.788 
Fit side-chains
REVERT: A  555 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7123 (ttt)
REVERT: A  629 PHE cc_start: 0.8092 (t80) cc_final: 0.7140 (t80)
REVERT: B   20 ASP cc_start: 0.8450 (m-30) cc_final: 0.8024 (m-30)
REVERT: B   52 GLN cc_start: 0.7559 (mt0) cc_final: 0.7256 (tt0)
REVERT: B   89 GLN cc_start: 0.6714 (mp-120) cc_final: 0.6262 (mp-120)
REVERT: B  181 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7626 (mm-30)
REVERT: C   20 ASP cc_start: 0.7408 (m-30) cc_final: 0.7148 (m-30)
REVERT: C   44 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.7605 (mt0)
REVERT: C  164 THR cc_start: 0.8830 (OUTLIER) cc_final: 0.8510 (m)
  outliers start: 22
  outliers final: 14
  residues processed: 129
  average time/residue: 1.2259
  time to fit residues: 166.3483
Evaluate side-chains
  134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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  562 LEU
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   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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 19 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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
D  59 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.126538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.107250 restraints weight = 9673.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.84
r_work: 0.3347 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6793  Z= 0.185
  Angle     :  0.538   6.602   9218  Z= 0.287
  Chirality :  0.043   0.135   1079
  Planarity :  0.004   0.051   1160
  Dihedral  :  4.133  26.294    915
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 14.88 %
    Favored  : 82.20 %
  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:  1.16 (0.30), residues: 846
  helix:  2.58 (0.30), residues: 332
  sheet:  1.00 (0.41), residues: 168
  loop : -1.25 (0.32), residues: 346

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   0.025   0.002   PHE A 649 
 TYR   0.012   0.001   TYR A 402 
 ARG   0.008   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06305 (  313)
  hydrogen bonds       : angle       4.04631 (  891)
  SS BOND              : bond        0.00514 (    1)
  SS BOND              : angle       1.55713 (    2)
  covalent geometry    : bond        0.00443 ( 6792)
  covalent geometry    : angle       0.53727 ( 9216)

*********************** 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
  138 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.724 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8095 (ttm-80) cc_final: 0.7816 (ttt-90)
REVERT: A  629 PHE cc_start: 0.8047 (t80) cc_final: 0.7178 (t80)
REVERT: B   20 ASP cc_start: 0.8467 (m-30) cc_final: 0.8044 (m-30)
REVERT: B   52 GLN cc_start: 0.7513 (mt0) cc_final: 0.7193 (tt0)
REVERT: B   53 MET cc_start: 0.7193 (ttm) cc_final: 0.6984 (ttm)
REVERT: B   89 GLN cc_start: 0.6720 (mp-120) cc_final: 0.6266 (mp-120)
REVERT: B  151 GLU cc_start: 0.8069 (mp0) cc_final: 0.7519 (mp0)
REVERT: B  181 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7670 (mm-30)
REVERT: C   44 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7680 (mt0)
REVERT: C  164 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8542 (m)
  outliers start: 21
  outliers final: 14
  residues processed: 127
  average time/residue: 1.2520
  time to fit residues: 167.0396
Evaluate side-chains
  130 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
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  562 LEU
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   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  336 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 9 optimal weight:    0.3980
   chunk 70 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    0.3980
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0970
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C 259 GLN
C 268 ASN
C 293 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.127100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.107885 restraints weight = 9673.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.84
r_work: 0.3361 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6793  Z= 0.163
  Angle     :  0.523   6.192   9218  Z= 0.279
  Chirality :  0.042   0.132   1079
  Planarity :  0.003   0.050   1160
  Dihedral  :  4.068  28.347    915
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.99 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.30), residues: 846
  helix:  2.65 (0.30), residues: 332
  sheet:  1.04 (0.41), residues: 169
  loop : -1.26 (0.32), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  82 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.024   0.001   PHE A 649 
 TYR   0.010   0.001   TYR A 408 
 ARG   0.008   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05933 (  313)
  hydrogen bonds       : angle       3.98611 (  891)
  SS BOND              : bond        0.00371 (    1)
  SS BOND              : angle       1.24664 (    2)
  covalent geometry    : bond        0.00385 ( 6792)
  covalent geometry    : angle       0.52249 ( 9216)

*********************** 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
  139 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.740 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7502 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8025 (t80) cc_final: 0.7182 (t80)
REVERT: B   20 ASP cc_start: 0.8462 (m-30) cc_final: 0.8026 (m-30)
REVERT: B   52 GLN cc_start: 0.7493 (mt0) cc_final: 0.7256 (tt0)
REVERT: B   53 MET cc_start: 0.7223 (ttm) cc_final: 0.7014 (ttm)
REVERT: B   89 GLN cc_start: 0.6711 (mp-120) cc_final: 0.6253 (mp-120)
REVERT: B   98 GLU cc_start: 0.5993 (mm-30) cc_final: 0.5559 (mm-30)
REVERT: B  151 GLU cc_start: 0.8059 (mp0) cc_final: 0.7511 (mp0)
REVERT: B  181 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7671 (mm-30)
REVERT: C   44 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7711 (mt0)
REVERT: C  164 THR cc_start: 0.8819 (OUTLIER) cc_final: 0.8502 (m)
  outliers start: 18
  outliers final: 14
  residues processed: 131
  average time/residue: 1.2544
  time to fit residues: 172.7123
Evaluate side-chains
  132 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.745 
-------------------------------------------------------------------------------
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  562 LEU
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   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  336 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 14 optimal weight:    0.4980
   chunk 6 optimal weight:    0.1980
   chunk 52 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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
C 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.126836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.107548 restraints weight = 9671.190|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.84
r_work: 0.3354 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
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      :  0.004   0.043   6793  Z= 0.177
  Angle     :  0.541   8.093   9218  Z= 0.287
  Chirality :  0.043   0.135   1079
  Planarity :  0.003   0.051   1160
  Dihedral  :  4.096  27.598    915
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.72 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.21 (0.30), residues: 846
  helix:  2.65 (0.30), residues: 330
  sheet:  1.04 (0.41), residues: 168
  loop : -1.25 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  82 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.024   0.002   PHE A 649 
 TYR   0.010   0.001   TYR A 402 
 ARG   0.007   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06178 (  313)
  hydrogen bonds       : angle       3.99005 (  891)
  SS BOND              : bond        0.00435 (    1)
  SS BOND              : angle       1.39599 (    2)
  covalent geometry    : bond        0.00421 ( 6792)
  covalent geometry    : angle       0.54106 ( 9216)

*********************** 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
  131 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7510 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8024 (t80) cc_final: 0.7202 (t80)
REVERT: B   52 GLN cc_start: 0.7495 (mt0) cc_final: 0.7256 (tt0)
REVERT: B   89 GLN cc_start: 0.6739 (mp-120) cc_final: 0.6253 (mp-120)
REVERT: B   98 GLU cc_start: 0.6020 (mm-30) cc_final: 0.5561 (mm-30)
REVERT: B  151 GLU cc_start: 0.8063 (mp0) cc_final: 0.7485 (mp0)
REVERT: B  181 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7678 (mm-30)
REVERT: C   44 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7756 (mt0)
REVERT: C  164 THR cc_start: 0.8832 (OUTLIER) cc_final: 0.8523 (m)
  outliers start: 19
  outliers final: 15
  residues processed: 122
  average time/residue: 1.3931
  time to fit residues: 177.8528
Evaluate side-chains
  133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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  562 LEU
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   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  187 VAL
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 71 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   chunk 9 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 61 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.127609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.108344 restraints weight = 9811.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.87
r_work: 0.3368 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6793  Z= 0.147
  Angle     :  0.518   7.574   9218  Z= 0.275
  Chirality :  0.042   0.130   1079
  Planarity :  0.003   0.050   1160
  Dihedral  :  3.934  21.256    915
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.55 %
    Favored  : 81.22 %
  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:  1.22 (0.30), residues: 846
  helix:  2.63 (0.30), residues: 337
  sheet:  1.06 (0.41), residues: 169
  loop : -1.31 (0.31), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.023   0.001   PHE A 649 
 TYR   0.009   0.001   TYR A 408 
 ARG   0.007   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05600 (  313)
  hydrogen bonds       : angle       3.88244 (  891)
  SS BOND              : bond        0.00365 (    1)
  SS BOND              : angle       1.14966 (    2)
  covalent geometry    : bond        0.00341 ( 6792)
  covalent geometry    : angle       0.51795 ( 9216)

********************** 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
  137 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 121
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7495 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8006 (t80) cc_final: 0.7179 (t80)
REVERT: B   20 ASP cc_start: 0.8443 (m-30) cc_final: 0.8018 (m-30)
REVERT: B   52 GLN cc_start: 0.7457 (mt0) cc_final: 0.7221 (tt0)
REVERT: B   89 GLN cc_start: 0.6835 (mp-120) cc_final: 0.6357 (mp-120)
REVERT: B   98 GLU cc_start: 0.6000 (mm-30) cc_final: 0.5583 (mm-30)
REVERT: B  151 GLU cc_start: 0.8054 (mp0) cc_final: 0.7529 (mp0)
REVERT: B  181 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7665 (mm-30)
REVERT: C   44 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7783 (mt0)
REVERT: C  164 THR cc_start: 0.8779 (OUTLIER) cc_final: 0.8471 (m)
  outliers start: 16
  outliers final: 12
  residues processed: 132
  average time/residue: 1.2777
  time to fit residues: 177.4063
Evaluate side-chains
  133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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  590 ILE
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  187 VAL
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 18 optimal weight:    0.4980
   chunk 78 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 64 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 49 optimal weight:    0.2980
   chunk 17 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   chunk 2 optimal weight:    0.2980
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.125149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.106093 restraints weight = 9809.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.86
r_work: 0.3378 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6793  Z= 0.135
  Angle     :  0.507   7.452   9218  Z= 0.270
  Chirality :  0.041   0.129   1079
  Planarity :  0.003   0.049   1160
  Dihedral  :  3.879  29.768    915
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.39 %
    Favored  : 80.67 %
  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:  1.25 (0.30), residues: 846
  helix:  2.67 (0.30), residues: 338
  sheet:  1.03 (0.41), residues: 169
  loop : -1.29 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.022   0.001   PHE A 649 
 TYR   0.023   0.001   TYR A 495 
 ARG   0.007   0.000   ARG B 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05363 (  313)
  hydrogen bonds       : angle       3.81281 (  891)
  SS BOND              : bond        0.00305 (    1)
  SS BOND              : angle       1.00058 (    2)
  covalent geometry    : bond        0.00308 ( 6792)
  covalent geometry    : angle       0.50731 ( 9216)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7243.34 seconds
wall clock time: 126 minutes 13.29 seconds (7573.29 seconds total)