Starting phenix.real_space_refine
on Tue Feb 11 21:19:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sf8_25077/02_2025/7sf8_25077_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sf8_25077/02_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_25077/02_2025/7sf8_25077.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sf8_25077/02_2025/7sf8_25077.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sf8_25077/02_2025/7sf8_25077_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sf8_25077/02_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-5592/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: 5.02, per 1000 atoms: 0.75
  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: 1.36
  Conformation dependent library (CDL) restraints added in 824.3 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: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.625A  pdb=" N   VAL A 387 " --> pdb=" O   TYR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 427
      removed outlier: 3.640A  pdb=" N   HIS A 401 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TYR A 402 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 464
      removed outlier: 3.901A  pdb=" N   LYS A 438 " --> pdb=" O   ASP A 434 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A 456 " --> pdb=" O   THR A 452 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   SER A 457 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   GLU A 458 " --> pdb=" O   PHE A 454 " (cutoff:3.500A)
      Proline residue:  A 459  - end of helix
      removed outlier: 3.580A  pdb=" N   LEU A 462 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   THR A 463 " --> pdb=" O   PRO A 459 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   GLY A 464 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 499
      removed outlier: 4.173A  pdb=" N   ALA A 473 " --> pdb=" O   CYS A 469 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE A 474 " --> pdb=" O   ARG A 470 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   CYS A 483 " --> pdb=" O   SER A 479 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   SER A 485 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 529
      removed outlier: 3.585A  pdb=" N   MET A 516 " --> pdb=" O   LYS A 512 " (cutoff:3.500A)
      Proline residue:  A 521  - end of helix
    Processing helix  chain 'A' and resid 532 through 534
      No H-bonds generated for 'chain 'A' and resid 532 through 534'
    Processing helix  chain 'A' and resid 560 through 568
      removed outlier: 4.043A  pdb=" N   SER A 564 " --> pdb=" O   ASP A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 591
    Processing helix  chain 'A' and resid 602 through 614
    Processing helix  chain 'A' and resid 615 through 625
      removed outlier: 4.055A  pdb=" N   PHE A 624 " --> pdb=" O   PHE A 621 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 643
      removed outlier: 3.518A  pdb=" N   VAL A 633 " --> pdb=" O   PHE A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'B' and resid 12 through 26
      removed outlier: 3.579A  pdb=" N   SER B  16 " --> pdb=" O   ALA B  12 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   GLU B  26 " --> pdb=" O   CYS B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 32
      removed outlier: 3.679A  pdb=" N   VAL B  30 " --> pdb=" O   GLU B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 52
    Processing helix  chain 'B' and resid 117 through 130
      removed outlier: 3.607A  pdb=" N   SER B 121 " --> pdb=" O   ARG B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 153
    Processing helix  chain 'B' and resid 157 through 161
    Processing helix  chain 'B' and resid 171 through 185
    Processing helix  chain 'B' and resid 206 through 228
      removed outlier: 3.708A  pdb=" N   ASP B 222 " --> pdb=" O   THR B 218 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLN B 226 " --> pdb=" O   ASP B 222 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU B 227 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 25
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'D' and resid 10 through 24
      removed outlier: 3.540A  pdb=" N   ASN D  24 " --> pdb=" O   LYS D  20 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 536 through 537
    Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 75
      removed outlier: 3.552A  pdb=" N   VAL B  34 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 6.901A  pdb=" N   LYS B  35 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   LEU B 107 " --> pdb=" O   LYS B  35 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   LEU B  37 " --> pdb=" O   LEU B 107 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   LEU B 109 " --> pdb=" O   LEU B  37 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   LEU B  39 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.755A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   CYS C 317 " --> pdb=" O   GLY C 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63
      removed outlier: 4.057A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU C  70 " --> pdb=" O   TRP C  82 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   SER C  74 " --> pdb=" O   LYS C  78 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.716A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.084A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   CYS C 121 " --> pdb=" O   GLU C 138 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   GLU C 138 " --> pdb=" O   CYS C 121 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ILE C 123 " --> pdb=" O   SER C 136 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG C 134 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.751A  pdb=" N   SER C 160 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   CYS C 149 " --> pdb=" O   VAL C 158 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   VAL C 158 " --> pdb=" O   CYS C 149 " (cutoff:3.500A)
      removed outlier: 5.225A  pdb=" N   PHE C 151 " --> pdb=" O   GLN C 156 " (cutoff:3.500A)
      removed outlier: 7.681A  pdb=" N   GLN C 156 " --> pdb=" O   PHE C 151 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ILE C 157 " --> pdb=" O   TRP C 169 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR C 178 " --> pdb=" O   LEU C 168 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.787A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.161A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE C 199 " --> pdb=" O   TRP C 211 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   SER C 207 " --> pdb=" O   ALA C 203 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   GLN C 220 " --> pdb=" O   LEU C 210 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.842A  pdb=" N   GLY C 244 " --> pdb=" O   ASN C 230 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   ILE C 232 " --> pdb=" O   ALA C 242 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   ALA C 242 " --> pdb=" O   ILE C 232 " (cutoff:3.500A)
      removed outlier: 4.862A  pdb=" N   PHE C 234 " --> pdb=" O   ALA C 240 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ALA C 240 " --> pdb=" O   PHE C 234 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   MET C 262 " --> pdb=" O   LEU C 252 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   ASP C 254 " --> pdb=" O   GLU C 260 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   GLU C 260 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.785A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLY C 306 " --> pdb=" O   VAL C 296 " (cutoff:3.500A)
      removed outlier: 5.721A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.441A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)

    313 hydrogen bonds defined for protein.
    891 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 1.65 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:             4.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.290
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076   6792  Z= 0.347
  Angle     :  0.740   7.037   9216  Z= 0.475
  Chirality :  0.050   0.282   1079
  Planarity :  0.004   0.054   1160
  Dihedral  : 13.034  86.064   2384
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.97 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.30), residues: 846
  helix:  1.57 (0.30), residues: 341
  sheet:  0.81 (0.41), residues: 161
  loop : -1.40 (0.31), residues: 344

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

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

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A  506 VAL cc_start: 0.8055 (t) cc_final: 0.7849 (t)
REVERT: A  520 PHE cc_start: 0.7693 (t80) cc_final: 0.7443 (t80)
REVERT: A  580 MET cc_start: 0.8415 (mmm) cc_final: 0.8156 (mmt)
REVERT: A  590 ILE cc_start: 0.8046 (mm) cc_final: 0.7796 (mp)
REVERT: B   89 GLN cc_start: 0.6281 (mp-120) cc_final: 0.6060 (mp-120)
REVERT: B  147 ASP cc_start: 0.7144 (p0) cc_final: 0.6789 (p0)
REVERT: B  151 GLU cc_start: 0.7436 (mp0) cc_final: 0.6841 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 141
  average time/residue: 1.3301
  time to fit residues: 196.0395
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  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  559 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0470
   chunk 34 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.5278

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.128494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.108932 restraints weight = 9743.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.3474 rms_B_bonded: 1.87
r_work: 0.3389 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3265 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1845

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

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 10.43 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.30), residues: 846
  helix:  1.85 (0.30), residues: 349
  sheet:  1.02 (0.40), residues: 171
  loop : -1.37 (0.33), residues: 326

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

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

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A  555 MET cc_start: 0.7520 (tmm) cc_final: 0.7229 (ttp)
REVERT: A  562 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7663 (tp)
REVERT: A  629 PHE cc_start: 0.8087 (t80) cc_final: 0.7592 (t80)
REVERT: B   20 ASP cc_start: 0.8479 (m-30) cc_final: 0.8090 (m-30)
REVERT: B   52 GLN cc_start: 0.7600 (mt0) cc_final: 0.7342 (tt0)
REVERT: B   89 GLN cc_start: 0.6564 (mp-120) cc_final: 0.6350 (mp-120)
REVERT: B  151 GLU cc_start: 0.8027 (mp0) cc_final: 0.7417 (mp0)
REVERT: C  164 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8418 (m)
  outliers start: 10
  outliers final: 2
  residues processed: 135
  average time/residue: 1.2344
  time to fit residues: 175.4870
Evaluate side-chains
  111 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 0.683 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  393 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:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 15 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0370
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.126852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.107384 restraints weight = 9785.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 1.84
r_work: 0.3362 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6792  Z= 0.237
  Angle     :  0.517   6.062   9216  Z= 0.279
  Chirality :  0.042   0.137   1079
  Planarity :  0.003   0.052   1160
  Dihedral  :  4.097  17.262    915
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 11.82 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.31), residues: 846
  helix:  1.98 (0.30), residues: 350
  sheet:  1.04 (0.40), residues: 173
  loop : -1.35 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  82 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.023   0.001   PHE A 649 
 TYR   0.011   0.001   TYR A 408 
 ARG   0.003   0.000   ARG C  49 

*********************** 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
  139 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8095 (ttt-90) cc_final: 0.7625 (ttp-170)
REVERT: A  555 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7150 (ttt)
REVERT: A  646 PHE cc_start: 0.7987 (t80) cc_final: 0.7509 (t80)
REVERT: B   20 ASP cc_start: 0.8448 (m-30) cc_final: 0.8006 (m-30)
REVERT: B   52 GLN cc_start: 0.7574 (mt0) cc_final: 0.7276 (tt0)
REVERT: B   89 GLN cc_start: 0.6608 (mp-120) cc_final: 0.6319 (mp-120)
REVERT: B  213 ARG cc_start: 0.7638 (mtt90) cc_final: 0.7285 (mtt90)
REVERT: C   40 VAL cc_start: 0.8838 (t) cc_final: 0.8637 (m)
REVERT: C  164 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8424 (m)
  outliers start: 19
  outliers final: 9
  residues processed: 128
  average time/residue: 1.4153
  time to fit residues: 191.3906
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  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  555 MET
Chi-restraints excluded: chain A residue  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 12 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 79 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3709 r_free = 0.3709 target = 0.125574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.106008 restraints weight = 9821.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.87
r_work: 0.3337 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6792  Z= 0.300
  Angle     :  0.552   7.158   9216  Z= 0.294
  Chirality :  0.044   0.139   1079
  Planarity :  0.004   0.053   1160
  Dihedral  :  4.200  17.569    915
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.91 %
    Favored  : 83.87 %
  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:  1.97 (0.30), residues: 350
  sheet:  0.98 (0.40), residues: 173
  loop : -1.36 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  82 
 HIS   0.006   0.001   HIS A 401 
 PHE   0.026   0.002   PHE A 649 
 TYR   0.011   0.001   TYR A 384 
 ARG   0.002   0.000   ARG C  49 

*********************** 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
  138 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 122
  time to evaluate  : 0.800 
Fit side-chains
REVERT: A  629 PHE cc_start: 0.8144 (t80) cc_final: 0.7695 (t80)
REVERT: B   20 ASP cc_start: 0.8454 (m-30) cc_final: 0.8012 (m-30)
REVERT: B   52 GLN cc_start: 0.7584 (mt0) cc_final: 0.7283 (tt0)
REVERT: B   89 GLN cc_start: 0.6701 (mp-120) cc_final: 0.6292 (mp-120)
REVERT: B  181 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7643 (mm-30)
REVERT: B  213 ARG cc_start: 0.7742 (mtt90) cc_final: 0.7536 (mtt90)
REVERT: C   20 ASP cc_start: 0.7377 (m-30) cc_final: 0.7125 (m-30)
REVERT: C  164 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8524 (m)
  outliers start: 16
  outliers final: 11
  residues processed: 128
  average time/residue: 1.3747
  time to fit residues: 184.2484
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  : 0.777 
-------------------------------------------------------------------------------
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  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  189 SER
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 29 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 48 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0670
   overall best weight:    0.7318

-------------------------------------------------------------------------------
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 = 0.3706 r_free = 0.3706 target = 0.125264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.105763 restraints weight = 9773.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.85
r_work: 0.3334 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6792  Z= 0.319
  Angle     :  0.560   7.404   9216  Z= 0.298
  Chirality :  0.044   0.141   1079
  Planarity :  0.004   0.053   1160
  Dihedral  :  4.226  22.160    915
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 14.60 %
    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 (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:  0.90 (0.30), residues: 846
  helix:  2.18 (0.30), residues: 339
  sheet:  0.91 (0.41), residues: 168
  loop : -1.29 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  82 
 HIS   0.005   0.001   HIS A 401 
 PHE   0.026   0.002   PHE A 649 
 TYR   0.011   0.001   TYR A 408 
 ARG   0.003   0.000   ARG C 134 

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

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8104 (ttt-90) cc_final: 0.7593 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8109 (t80) cc_final: 0.7234 (t80)
REVERT: B   52 GLN cc_start: 0.7534 (mt0) cc_final: 0.7228 (tt0)
REVERT: B   89 GLN cc_start: 0.6737 (mp-120) cc_final: 0.6284 (mp-120)
REVERT: B  151 GLU cc_start: 0.8057 (mp0) cc_final: 0.7503 (mp0)
REVERT: B  181 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7616 (mm-30)
REVERT: C   20 ASP cc_start: 0.7418 (m-30) cc_final: 0.7163 (m-30)
REVERT: C   44 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7644 (mt0)
REVERT: C  164 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8550 (m)
  outliers start: 22
  outliers final: 13
  residues processed: 129
  average time/residue: 1.3018
  time to fit residues: 176.3013
Evaluate side-chains
  132 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
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  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  164 THR
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  228 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0040
   chunk 11 optimal weight:    0.1980
   chunk 7 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 1 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 0 optimal weight:    0.0980
   overall best weight:    0.3392

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.128342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.109248 restraints weight = 9637.041|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.84
r_work: 0.3384 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6792  Z= 0.174
  Angle     :  0.487   6.063   9216  Z= 0.260
  Chirality :  0.041   0.128   1079
  Planarity :  0.003   0.048   1160
  Dihedral  :  3.955  27.445    915
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.44 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.30), residues: 846
  helix:  2.53 (0.30), residues: 338
  sheet:  0.98 (0.41), residues: 169
  loop : -1.26 (0.32), 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   0.021   0.001   PHE A 649 
 TYR   0.009   0.001   TYR A 408 
 ARG   0.004   0.000   ARG C 134 

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

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

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

  1692 Ramachandran restraints generated.
    846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.699 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8006 (ttt-90) cc_final: 0.7546 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8014 (t80) cc_final: 0.7209 (t80)
REVERT: B   20 ASP cc_start: 0.8419 (m-30) cc_final: 0.7977 (m-30)
REVERT: B   52 GLN cc_start: 0.7455 (mt0) cc_final: 0.7241 (tt0)
REVERT: B   89 GLN cc_start: 0.6815 (mp-120) cc_final: 0.6366 (mp-120)
REVERT: B  181 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7651 (mm-30)
REVERT: C  164 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8398 (m)
  outliers start: 19
  outliers final: 11
  residues processed: 129
  average time/residue: 1.2791
  time to fit residues: 173.1902
Evaluate side-chains
  121 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 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 C residue   37 ILE
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 34 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 68 optimal weight:    0.5980
   chunk 24 optimal weight:    0.2980
   chunk 30 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.126748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.107518 restraints weight = 9649.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 1.83
r_work: 0.3356 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
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   0.043   6792  Z= 0.269
  Angle     :  0.534   6.509   9216  Z= 0.284
  Chirality :  0.043   0.133   1079
  Planarity :  0.003   0.050   1160
  Dihedral  :  4.070  25.770    915
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.86 %
    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 (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:  1.11 (0.30), residues: 846
  helix:  2.50 (0.30), residues: 339
  sheet:  0.97 (0.41), residues: 168
  loop : -1.32 (0.32), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C  82 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.024   0.002   PHE A 649 
 TYR   0.024   0.001   TYR A 495 
 ARG   0.004   0.000   ARG B 209 

*********************** 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
  136 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.704 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8071 (ttt-90) cc_final: 0.7570 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8030 (t80) cc_final: 0.7190 (t80)
REVERT: B   52 GLN cc_start: 0.7478 (mt0) cc_final: 0.7265 (tt0)
REVERT: B   89 GLN cc_start: 0.6718 (mp-120) cc_final: 0.6239 (mp-120)
REVERT: B  151 GLU cc_start: 0.8057 (mp0) cc_final: 0.7517 (mp0)
REVERT: B  181 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7675 (mm-30)
REVERT: C   35 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8076 (m-40)
REVERT: C   44 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7841 (mt0)
REVERT: C  164 THR cc_start: 0.8817 (OUTLIER) cc_final: 0.8509 (m)
  outliers start: 17
  outliers final: 13
  residues processed: 128
  average time/residue: 1.3273
  time to fit residues: 177.9509
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  : 0.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 VAL
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  531 VAL
Chi-restraints excluded: chain A residue  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   35 ASN
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:    0.9990
   chunk 70 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.7784

-------------------------------------------------------------------------------
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 = 0.3715 r_free = 0.3715 target = 0.125990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.106672 restraints weight = 9671.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.85
r_work: 0.3341 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6792  Z= 0.338
  Angle     :  0.574   7.229   9216  Z= 0.304
  Chirality :  0.045   0.143   1079
  Planarity :  0.004   0.052   1160
  Dihedral  :  4.206  22.281    915
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.83 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.30), residues: 846
  helix:  2.19 (0.30), residues: 348
  sheet:  0.95 (0.41), residues: 168
  loop : -1.37 (0.32), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C  82 
 HIS   0.004   0.001   HIS A 401 
 PHE   0.026   0.002   PHE A 649 
 TYR   0.023   0.002   TYR A 495 
 ARG   0.011   0.000   ARG B 209 

*********************** 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: 16
    poor density    : 117
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8121 (ttt-90) cc_final: 0.7592 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8060 (t80) cc_final: 0.7248 (t80)
REVERT: B   52 GLN cc_start: 0.7518 (mt0) cc_final: 0.7280 (tt0)
REVERT: B   89 GLN cc_start: 0.6770 (mp-120) cc_final: 0.6287 (mp-120)
REVERT: B   98 GLU cc_start: 0.6083 (mm-30) cc_final: 0.5689 (mm-30)
REVERT: B  151 GLU cc_start: 0.8069 (mp0) cc_final: 0.7474 (mp0)
REVERT: B  181 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7659 (mm-30)
REVERT: C   35 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8048 (m-40)
REVERT: C   44 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7922 (mt0)
REVERT: C  164 THR cc_start: 0.8866 (OUTLIER) cc_final: 0.8580 (m)
  outliers start: 16
  outliers final: 12
  residues processed: 125
  average time/residue: 1.3811
  time to fit residues: 180.9646
Evaluate side-chains
  123 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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  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   35 ASN
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:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 38 optimal weight:    0.3980
   chunk 14 optimal weight:    0.6980
   chunk 6 optimal weight:    0.2980
   chunk 52 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   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 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 = 0.3731 r_free = 0.3731 target = 0.127175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.107954 restraints weight = 9674.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3450 rms_B_bonded: 1.84
r_work: 0.3360 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6792  Z= 0.246
  Angle     :  0.535   6.961   9216  Z= 0.284
  Chirality :  0.042   0.132   1079
  Planarity :  0.003   0.050   1160
  Dihedral  :  4.026  17.537    915
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.97 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.30), residues: 846
  helix:  2.54 (0.30), residues: 337
  sheet:  0.98 (0.41), residues: 168
  loop : -1.29 (0.31), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C  82 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.023   0.001   PHE A 649 
 TYR   0.021   0.001   TYR A 495 
 ARG   0.012   0.000   ARG B 209 

*********************** 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
  137 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.790 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.8068 (ttt-90) cc_final: 0.7573 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8027 (t80) cc_final: 0.7228 (t80)
REVERT: B   20 ASP cc_start: 0.8413 (m-30) cc_final: 0.7959 (m-30)
REVERT: B   52 GLN cc_start: 0.7480 (mt0) cc_final: 0.7244 (tt0)
REVERT: B   89 GLN cc_start: 0.6852 (mp-120) cc_final: 0.6346 (mp-120)
REVERT: B  151 GLU cc_start: 0.8044 (mp0) cc_final: 0.7511 (mp0)
REVERT: B  181 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7684 (mm-30)
REVERT: C   35 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.8075 (m-40)
REVERT: C  164 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8510 (m)
  outliers start: 15
  outliers final: 11
  residues processed: 131
  average time/residue: 1.2841
  time to fit residues: 176.7922
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  : 0.687 
-------------------------------------------------------------------------------
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  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   35 ASN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 8 optimal weight:    0.4980
   chunk 20 optimal weight:    0.5980
   chunk 21 optimal weight:    0.1980
   chunk 9 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 44 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0030
   overall best weight:    0.3190

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.128662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.109612 restraints weight = 9780.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.85
r_work: 0.3388 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3260 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6792  Z= 0.172
  Angle     :  0.507   7.410   9216  Z= 0.269
  Chirality :  0.041   0.127   1079
  Planarity :  0.004   0.054   1160
  Dihedral  :  3.841  18.735    915
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.52 %
    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:  1.27 (0.30), residues: 846
  helix:  2.68 (0.30), residues: 338
  sheet:  1.01 (0.40), residues: 169
  loop : -1.25 (0.31), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 486 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.021   0.001   PHE A 649 
 TYR   0.025   0.001   TYR A 495 
 ARG   0.014   0.001   ARG B 209 

********************** 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
  127 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A  496 ARG cc_start: 0.7997 (ttt-90) cc_final: 0.7505 (ttp-170)
REVERT: A  629 PHE cc_start: 0.8007 (t80) cc_final: 0.7177 (t80)
REVERT: B   20 ASP cc_start: 0.8381 (m-30) cc_final: 0.7924 (m-30)
REVERT: B   52 GLN cc_start: 0.7461 (mt0) cc_final: 0.7217 (tt0)
REVERT: B   89 GLN cc_start: 0.6845 (mp-120) cc_final: 0.6432 (mp-120)
REVERT: B  181 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7680 (mm-30)
REVERT: C  164 THR cc_start: 0.8710 (OUTLIER) cc_final: 0.8384 (m)
  outliers start: 13
  outliers final: 10
  residues processed: 122
  average time/residue: 1.3745
  time to fit residues: 176.2517
Evaluate side-chains
  124 residues out of total 748 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
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 C residue   42 ARG
Chi-restraints excluded: chain C residue   78 LYS
Chi-restraints excluded: chain C residue  164 THR
Chi-restraints excluded: chain C residue  336 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 78 optimal weight:    0.3980
   chunk 56 optimal weight:    0.1980
   chunk 64 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0470
   chunk 9 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   overall best weight:    0.3678

-------------------------------------------------------------------------------
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 = 0.3749 r_free = 0.3749 target = 0.128441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.109369 restraints weight = 9767.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 1.86
r_work: 0.3383 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6792  Z= 0.187
  Angle     :  0.511   6.266   9216  Z= 0.270
  Chirality :  0.041   0.129   1079
  Planarity :  0.004   0.062   1160
  Dihedral  :  3.808  17.594    915
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 3.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.66 %
    Favored  : 80.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.30), residues: 846
  helix:  2.73 (0.30), residues: 337
  sheet:  1.03 (0.40), residues: 169
  loop : -1.23 (0.32), 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   0.021   0.001   PHE A 649 
 TYR   0.008   0.001   TYR A 408 
 ARG   0.013   0.001   ARG B 209 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6402.91 seconds
wall clock time: 113 minutes 32.06 seconds (6812.06 seconds total)