Starting phenix.real_space_refine
on Tue Mar  3 15:35:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sf8_25077/03_2026/7sf8_25077_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sf8_25077/03_2026/7sf8_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_25077/03_2026/7sf8_25077.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sf8_25077/03_2026/7sf8_25077.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sf8_25077/03_2026/7sf8_25077_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sf8_25077/03_2026/7sf8_25077_neut.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'ARG:plan': 5, 'TRP:plan': 1, 'GLN:plan1': 2}
          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: 1.69, per 1000 atoms: 0.25
  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: 0.69
  Conformation dependent library (CDL) restraints added in 200.6 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      42.3% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  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: 1.06

  Time building geometry restraints manager: 0.89 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:             5.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.240
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:8.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.040
-------------------------------------------------------------------------------
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 : 4.32
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.000   ARG A 559 
 TYR   0.014   0.002   TYR A 408 
 PHE   0.021   0.002   PHE A 649 
 TRP   0.011   0.001   TRP C  82 
 HIS   0.004   0.001   HIS B 221 

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

*********************** 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  : 0.245 
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: 0.6059 (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: 0.6822
  time to fit residues: 100.3570
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  : 0.321 
-------------------------------------------------------------------------------
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 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.2980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.4980
   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 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 = 0.3742 r_free = 0.3742 target = 0.127894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.108317 restraints weight = 9813.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.85
r_work: 0.3382 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6793  Z= 0.174
  Angle     :  0.552   5.600   9218  Z= 0.298
  Chirality :  0.043   0.135   1079
  Planarity :  0.004   0.055   1160
  Dihedral  :  4.551  51.354    919
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.29 %
    Favored  : 88.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.30), residues: 846
  helix:  1.84 (0.30), residues: 349
  sheet:  1.02 (0.41), residues: 171
  loop : -1.37 (0.33), residues: 326

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 6792)
  covalent geometry    : angle       0.55141 ( 9216)
  SS BOND              : bond        0.00677 (    1)
  SS BOND              : angle       1.92887 (    2)
  hydrogen bonds       : bond        0.06481 (  313)
  hydrogen bonds       : angle       4.20782 (  891)

*********************** 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
  141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  555 MET cc_start: 0.7565 (tmm) cc_final: 0.7287 (ttp)
REVERT: A  562 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7675 (tp)
REVERT: A  580 MET cc_start: 0.8773 (mmm) cc_final: 0.8566 (mmt)
REVERT: A  629 PHE cc_start: 0.8121 (t80) cc_final: 0.7552 (t80)
REVERT: B   20 ASP cc_start: 0.8447 (m-30) cc_final: 0.8056 (m-30)
REVERT: B   52 GLN cc_start: 0.7601 (mt0) cc_final: 0.7339 (tt0)
REVERT: B   89 GLN cc_start: 0.6562 (mp-120) cc_final: 0.6354 (mp-120)
REVERT: C  164 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8422 (m)
  outliers start: 12
  outliers final: 3
  residues processed: 133
  average time/residue: 0.5737
  time to fit residues: 80.1379
Evaluate side-chains
  112 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
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 B residue  228 MET
Chi-restraints excluded: chain C residue  164 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0000
   chunk 54 optimal weight:    0.9980
   chunk 55 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 21 optimal weight:    0.4980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.5384

-------------------------------------------------------------------------------
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 = 0.127033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.107617 restraints weight = 9693.168|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.83
r_work: 0.3358 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2501

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= 0.166
  Angle     :  0.523   6.138   9218  Z= 0.282
  Chirality :  0.043   0.138   1079
  Planarity :  0.003   0.052   1160
  Dihedral  :  4.138  17.384    915
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.82 %
    Favored  : 85.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.31), residues: 846
  helix:  1.96 (0.30), residues: 350
  sheet:  1.03 (0.40), residues: 173
  loop : -1.35 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 219 
 TYR   0.010   0.001   TYR A 408 
 PHE   0.024   0.002   PHE A 649 
 TRP   0.011   0.001   TRP C  82 
 HIS   0.005   0.001   HIS B 221 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 6792)
  covalent geometry    : angle       0.52281 ( 9216)
  SS BOND              : bond        0.00495 (    1)
  SS BOND              : angle       1.57120 (    2)
  hydrogen bonds       : bond        0.06215 (  313)
  hydrogen bonds       : angle       4.06393 (  891)

*********************** 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
  136 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8094 (ttt-90) cc_final: 0.7588 (ttp-170)
REVERT: A  555 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7147 (ttt)
REVERT: A  580 MET cc_start: 0.8717 (mmm) cc_final: 0.8496 (mmt)
REVERT: B   20 ASP cc_start: 0.8433 (m-30) cc_final: 0.8002 (m-30)
REVERT: B   52 GLN cc_start: 0.7572 (mt0) cc_final: 0.7281 (tt0)
REVERT: B   89 GLN cc_start: 0.6676 (mp-120) cc_final: 0.6396 (mp-120)
REVERT: B  213 ARG cc_start: 0.7640 (mtt90) cc_final: 0.7294 (mtt90)
REVERT: C  164 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8439 (m)
  outliers start: 17
  outliers final: 8
  residues processed: 125
  average time/residue: 0.6358
  time to fit residues: 83.2156
Evaluate side-chains
  126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
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  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  164 THR
Chi-restraints excluded: chain C residue  228 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 67 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0050
   chunk 49 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
C  35 ASN
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 = 0.3715 r_free = 0.3715 target = 0.126028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.106515 restraints weight = 9898.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.88
r_work: 0.3349 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3220 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2755

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= 0.177
  Angle     :  0.533   6.879   9218  Z= 0.285
  Chirality :  0.043   0.137   1079
  Planarity :  0.004   0.052   1160
  Dihedral  :  4.128  17.274    915
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.35 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.30), residues: 846
  helix:  2.23 (0.30), residues: 339
  sheet:  0.98 (0.40), residues: 173
  loop : -1.31 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  96 
 TYR   0.011   0.001   TYR A 384 
 PHE   0.025   0.002   PHE A 649 
 TRP   0.013   0.002   TRP C  82 
 HIS   0.005   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 6792)
  covalent geometry    : angle       0.53308 ( 9216)
  SS BOND              : bond        0.00429 (    1)
  SS BOND              : angle       1.38569 (    2)
  hydrogen bonds       : bond        0.06257 (  313)
  hydrogen bonds       : angle       4.04754 (  891)

*********************** 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
  139 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 123
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  629 PHE cc_start: 0.8142 (t80) cc_final: 0.7633 (t80)
REVERT: A  646 PHE cc_start: 0.7781 (t80) cc_final: 0.7366 (t80)
REVERT: B   20 ASP cc_start: 0.8444 (m-30) cc_final: 0.8005 (m-30)
REVERT: B   52 GLN cc_start: 0.7572 (mt0) cc_final: 0.7288 (tt0)
REVERT: B   89 GLN cc_start: 0.6704 (mp-120) cc_final: 0.6333 (mp-120)
REVERT: B  181 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7614 (mm-30)
REVERT: C   20 ASP cc_start: 0.7380 (m-30) cc_final: 0.7129 (m-30)
REVERT: C  164 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8493 (m)
  outliers start: 16
  outliers final: 9
  residues processed: 130
  average time/residue: 0.6182
  time to fit residues: 84.2321
Evaluate side-chains
  127 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   chunk 54 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   chunk 43 optimal weight:    0.0050
   chunk 35 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.3794

-------------------------------------------------------------------------------
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 = 0.3745 r_free = 0.3745 target = 0.128100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.108878 restraints weight = 9864.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.86
r_work: 0.3377 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6793  Z= 0.130
  Angle     :  0.491   6.108   9218  Z= 0.263
  Chirality :  0.041   0.130   1079
  Planarity :  0.003   0.049   1160
  Dihedral  :  3.957  24.276    915
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.30), residues: 846
  helix:  2.41 (0.30), residues: 339
  sheet:  1.00 (0.40), residues: 174
  loop : -1.29 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  96 
 TYR   0.020   0.001   TYR A 495 
 PHE   0.022   0.001   PHE A 649 
 TRP   0.012   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6792)
  covalent geometry    : angle       0.49130 ( 9216)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       1.01435 (    2)
  hydrogen bonds       : bond        0.05357 (  313)
  hydrogen bonds       : angle       3.89267 (  891)

*********************** 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
  144 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.274 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8042 (ttt-90) cc_final: 0.7546 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8067 (t80) cc_final: 0.7231 (t80)
REVERT: B   20 ASP cc_start: 0.8460 (m-30) cc_final: 0.8023 (m-30)
REVERT: B   32 ARG cc_start: 0.8241 (ptp-170) cc_final: 0.7913 (ptp-170)
REVERT: B   52 GLN cc_start: 0.7511 (mt0) cc_final: 0.7222 (tt0)
REVERT: B   89 GLN cc_start: 0.6651 (mp-120) cc_final: 0.6235 (mp-120)
REVERT: B  181 GLU cc_start: 0.8001 (mm-30) cc_final: 0.7631 (mm-30)
REVERT: C   20 ASP cc_start: 0.7394 (m-30) cc_final: 0.7134 (m-30)
REVERT: C  164 THR cc_start: 0.8780 (OUTLIER) cc_final: 0.8423 (m)
  outliers start: 21
  outliers final: 10
  residues processed: 130
  average time/residue: 0.6218
  time to fit residues: 84.7005
Evaluate side-chains
  129 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  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  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 60 optimal weight:    0.3980
   chunk 32 optimal weight:    0.0000
   chunk 27 optimal weight:    0.0870
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 57 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 2 optimal weight:    0.0980
   chunk 79 optimal weight:    5.9990
   overall best weight:    0.2362

-------------------------------------------------------------------------------
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 = 0.3755 r_free = 0.3755 target = 0.126885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.108027 restraints weight = 9868.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.85
r_work: 0.3411 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   6793  Z= 0.106
  Angle     :  0.463   5.811   9218  Z= 0.248
  Chirality :  0.040   0.127   1079
  Planarity :  0.003   0.047   1160
  Dihedral  :  3.772  26.509    915
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.69 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.26 (0.31), residues: 846
  helix:  2.61 (0.30), residues: 339
  sheet:  1.12 (0.40), residues: 174
  loop : -1.30 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 213 
 TYR   0.024   0.001   TYR A 495 
 PHE   0.019   0.001   PHE A 649 
 TRP   0.010   0.001   TRP A 486 
 HIS   0.002   0.000   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 6792)
  covalent geometry    : angle       0.46311 ( 9216)
  SS BOND              : bond        0.00161 (    1)
  SS BOND              : angle       0.62115 (    2)
  hydrogen bonds       : bond        0.04571 (  313)
  hydrogen bonds       : angle       3.71047 (  891)

*********************** 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
  134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A  495 TYR cc_start: 0.8119 (t80) cc_final: 0.7883 (t80)
REVERT: A  496 ARG cc_start: 0.7952 (ttt-90) cc_final: 0.7502 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8011 (t80) cc_final: 0.7179 (t80)
REVERT: B   20 ASP cc_start: 0.8473 (m-30) cc_final: 0.8046 (m-30)
REVERT: B   89 GLN cc_start: 0.6816 (mp-120) cc_final: 0.6340 (mp-120)
REVERT: B   98 GLU cc_start: 0.5984 (mm-30) cc_final: 0.5550 (mm-30)
REVERT: B  181 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7654 (mm-30)
REVERT: C   20 ASP cc_start: 0.7372 (m-30) cc_final: 0.7109 (m-30)
REVERT: C  164 THR cc_start: 0.8678 (OUTLIER) cc_final: 0.8331 (m)
  outliers start: 11
  outliers final: 5
  residues processed: 129
  average time/residue: 0.6496
  time to fit residues: 87.7271
Evaluate side-chains
  126 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue   92 GLU
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 1 optimal weight:    0.0570
   chunk 17 optimal weight:    0.4980
   chunk 46 optimal weight:    0.0870
   chunk 41 optimal weight:    0.3980
   chunk 61 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.3276

-------------------------------------------------------------------------------
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 = 0.3743 r_free = 0.3743 target = 0.126075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.107176 restraints weight = 9700.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.82
r_work: 0.3399 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3273 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6793  Z= 0.120
  Angle     :  0.477   5.699   9218  Z= 0.254
  Chirality :  0.041   0.127   1079
  Planarity :  0.003   0.047   1160
  Dihedral  :  3.777  26.118    915
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 15.86 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.30 (0.30), residues: 846
  helix:  2.59 (0.30), residues: 345
  sheet:  1.14 (0.41), residues: 169
  loop : -1.25 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 213 
 TYR   0.022   0.001   TYR A 495 
 PHE   0.020   0.001   PHE A 649 
 TRP   0.011   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 6792)
  covalent geometry    : angle       0.47648 ( 9216)
  SS BOND              : bond        0.00266 (    1)
  SS BOND              : angle       0.89650 (    2)
  hydrogen bonds       : bond        0.04982 (  313)
  hydrogen bonds       : angle       3.75698 (  891)

*********************** 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
  134 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  495 TYR cc_start: 0.8167 (t80) cc_final: 0.7905 (t80)
REVERT: A  496 ARG cc_start: 0.7979 (ttt-90) cc_final: 0.7531 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8014 (t80) cc_final: 0.7185 (t80)
REVERT: B   20 ASP cc_start: 0.8451 (m-30) cc_final: 0.8020 (m-30)
REVERT: B   52 GLN cc_start: 0.7441 (mt0) cc_final: 0.7151 (tt0)
REVERT: B   89 GLN cc_start: 0.6841 (mp-120) cc_final: 0.6330 (mp-120)
REVERT: B  181 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7652 (mm-30)
REVERT: C   44 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7670 (mt0)
REVERT: C  164 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8354 (m)
  outliers start: 13
  outliers final: 9
  residues processed: 128
  average time/residue: 0.6464
  time to fit residues: 86.7030
Evaluate side-chains
  131 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  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   44 GLN
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 54 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9980
   chunk 1 optimal weight:    0.2980
   chunk 7 optimal weight:    0.5980
   chunk 28 optimal weight:    0.6980
   chunk 58 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   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
C 340 ASN
D  59 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.125400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.106302 restraints weight = 9753.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.86
r_work: 0.3381 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3253 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6793  Z= 0.133
  Angle     :  0.491   6.786   9218  Z= 0.261
  Chirality :  0.041   0.129   1079
  Planarity :  0.003   0.047   1160
  Dihedral  :  3.833  26.168    915
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.27 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.30), residues: 846
  helix:  2.73 (0.30), residues: 339
  sheet:  1.10 (0.41), residues: 169
  loop : -1.22 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 213 
 TYR   0.022   0.001   TYR A 495 
 PHE   0.021   0.001   PHE A 649 
 TRP   0.011   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 6792)
  covalent geometry    : angle       0.49031 ( 9216)
  SS BOND              : bond        0.00321 (    1)
  SS BOND              : angle       1.08814 (    2)
  hydrogen bonds       : bond        0.05329 (  313)
  hydrogen bonds       : angle       3.78592 (  891)

*********************** 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
  133 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7553 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8012 (t80) cc_final: 0.7163 (t80)
REVERT: B   20 ASP cc_start: 0.8458 (m-30) cc_final: 0.8027 (m-30)
REVERT: B   52 GLN cc_start: 0.7471 (mt0) cc_final: 0.7203 (tt0)
REVERT: B   89 GLN cc_start: 0.6725 (mp-120) cc_final: 0.6235 (mp-120)
REVERT: B  181 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7664 (mm-30)
REVERT: C   44 GLN cc_start: 0.8576 (OUTLIER) cc_final: 0.7828 (mt0)
REVERT: C  164 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8388 (m)
  outliers start: 13
  outliers final: 10
  residues processed: 125
  average time/residue: 0.6429
  time to fit residues: 84.1153
Evaluate side-chains
  123 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
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  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 B residue  228 MET
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue   44 GLN
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 2 optimal weight:    0.0970
   chunk 17 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0870
   chunk 16 optimal weight:    0.3980
   chunk 61 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0770
   overall best weight:    0.2314

-------------------------------------------------------------------------------
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 = 0.3774 r_free = 0.3774 target = 0.130253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.111266 restraints weight = 9745.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.85
r_work: 0.3415 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3290 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6793  Z= 0.104
  Angle     :  0.461   5.918   9218  Z= 0.246
  Chirality :  0.040   0.126   1079
  Planarity :  0.003   0.045   1160
  Dihedral  :  3.636  19.794    915
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.83 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.31), residues: 846
  helix:  2.90 (0.30), residues: 334
  sheet:  1.17 (0.42), residues: 168
  loop : -1.15 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 213 
 TYR   0.025   0.001   TYR A 495 
 PHE   0.020   0.001   PHE A 649 
 TRP   0.010   0.001   TRP A 486 
 HIS   0.002   0.000   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 6792)
  covalent geometry    : angle       0.46100 ( 9216)
  SS BOND              : bond        0.00168 (    1)
  SS BOND              : angle       0.60296 (    2)
  hydrogen bonds       : bond        0.04479 (  313)
  hydrogen bonds       : angle       3.62638 (  891)

*********************** 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
  119 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.255 
Fit side-chains
REVERT: A  495 TYR cc_start: 0.8130 (t80) cc_final: 0.7857 (t80)
REVERT: A  496 ARG cc_start: 0.7943 (ttt-90) cc_final: 0.7524 (ttp-170)
REVERT: A  629 PHE cc_start: 0.7977 (t80) cc_final: 0.7148 (t80)
REVERT: B   52 GLN cc_start: 0.7452 (mt0) cc_final: 0.7163 (tt0)
REVERT: B   89 GLN cc_start: 0.6856 (mp-120) cc_final: 0.6381 (mp-120)
REVERT: B  181 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7642 (mm-30)
REVERT: C  164 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8288 (m)
  outliers start: 10
  outliers final: 8
  residues processed: 115
  average time/residue: 0.6212
  time to fit residues: 74.8061
Evaluate side-chains
  124 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
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  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   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0020
   chunk 23 optimal weight:    0.3980
   overall best weight:    0.5188

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.127820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.108578 restraints weight = 9681.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 1.84
r_work: 0.3372 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3245 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3216

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= 0.160
  Angle     :  0.520   5.811   9218  Z= 0.277
  Chirality :  0.042   0.131   1079
  Planarity :  0.003   0.048   1160
  Dihedral  :  3.828  18.987    915
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 17.52 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.30), residues: 846
  helix:  2.69 (0.30), residues: 337
  sheet:  1.08 (0.41), residues: 169
  loop : -1.20 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 213 
 TYR   0.026   0.001   TYR A 495 
 PHE   0.023   0.001   PHE A 649 
 TRP   0.013   0.001   TRP C  82 
 HIS   0.004   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6792)
  covalent geometry    : angle       0.51969 ( 9216)
  SS BOND              : bond        0.00382 (    1)
  SS BOND              : angle       1.21424 (    2)
  hydrogen bonds       : bond        0.05837 (  313)
  hydrogen bonds       : angle       3.82940 (  891)

********************** 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
  120 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8052 (ttt-90) cc_final: 0.7560 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8003 (t80) cc_final: 0.7198 (t80)
REVERT: B   20 ASP cc_start: 0.8465 (m-30) cc_final: 0.8034 (m-30)
REVERT: B   52 GLN cc_start: 0.7480 (mt0) cc_final: 0.7203 (tt0)
REVERT: B   89 GLN cc_start: 0.6721 (mp-120) cc_final: 0.6207 (mp-120)
REVERT: B  181 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7663 (mm-30)
REVERT: C  164 THR cc_start: 0.8761 (OUTLIER) cc_final: 0.8449 (m)
  outliers start: 8
  outliers final: 7
  residues processed: 116
  average time/residue: 0.6286
  time to fit residues: 76.4339
Evaluate side-chains
  113 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 105
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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  633 VAL
Chi-restraints excluded: chain B residue    8 GLU
Chi-restraints excluded: chain B residue  164 GLU
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 70 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0570
   chunk 2 optimal weight:    0.2980
   chunk 1 optimal weight:    0.1980
   chunk 42 optimal weight:    0.1980
   chunk 56 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.2298

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.130489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.111498 restraints weight = 9565.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.83
r_work: 0.3417 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6793  Z= 0.104
  Angle     :  0.460   5.465   9218  Z= 0.247
  Chirality :  0.040   0.126   1079
  Planarity :  0.003   0.048   1160
  Dihedral  :  3.590  14.913    915
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.66 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.30), residues: 846
  helix:  2.92 (0.30), residues: 332
  sheet:  1.14 (0.42), residues: 168
  loop : -1.13 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 213 
 TYR   0.024   0.001   TYR A 495 
 PHE   0.020   0.001   PHE A 649 
 TRP   0.011   0.001   TRP A 486 
 HIS   0.003   0.000   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 6792)
  covalent geometry    : angle       0.46016 ( 9216)
  SS BOND              : bond        0.00154 (    1)
  SS BOND              : angle       0.60109 (    2)
  hydrogen bonds       : bond        0.04496 (  313)
  hydrogen bonds       : angle       3.61185 (  891)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3148.01 seconds
wall clock time: 54 minutes 10.44 seconds (3250.44 seconds total)