Starting phenix.real_space_refine
on Thu Mar 13 10:07:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c91_45359/03_2025/9c91_45359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c91_45359/03_2025/9c91_45359.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c91_45359/03_2025/9c91_45359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c91_45359/03_2025/9c91_45359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c91_45359/03_2025/9c91_45359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c91_45359/03_2025/9c91_45359.cif"
  }
  resolution = 2.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.054
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: 7
    Type Number    sf(0)   Gaussians
     K       1      8.98       5
     Fe      5      7.16       5
     P       4      5.49       5
     S      31      5.16       5
     C    5532      2.51       5
     N    1545      2.21       5
     O    1666      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8784
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4119
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 518, 4093
          Classifications: {'peptide': 518}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 496}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 518, 4093
          Classifications: {'peptide': 518}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 21, 'TRANS': 496}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 4146
    Chain: "B"
      Number of atoms: 4504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 570, 4504
          Classifications: {'peptide': 570}
          Link IDs: {'PCIS': 2, 'PTRANS': 25, 'TRANS': 542}
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 84
          Unusual residues: {'FAD': 1, 'FMN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 77
          Unusual residues: {'  K': 1, 'PO4': 1, 'SF4': 1, 'SRM': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unsupported chir.volume_sign: {'cros': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7575  SG  CYS B 434      31.093  38.242  41.422  1.00 35.39           S
  ATOM   7619  SG  CYS B 440      30.295  43.097  45.770  1.00 39.39           S
  ATOM   7919  SG  CYS B 479      25.725  42.645  42.397  1.00 45.34           S
  ATOM   7944  SG  CYS B 483      31.365  44.001  39.596  1.00 61.15           S
  ATOM   7944  SG  CYS B 483      31.365  44.001  39.596  1.00 61.15           S

  Time building chain proxies: 8.12, per 1000 atoms: 0.92
  Number of scatterers: 8784
  At special positions: 0
  Unit cell: (77.265, 86.445, 139.995, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Fe      5     26.01
     K       1     19.00
     S      31     16.00
     P       4     15.00
     O    1666      8.00
     N    1545      7.00
     C    5532      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=3, symmetry=0
  Number of additional bonds: simple=3, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.34
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 B 603 "
        pdb="FE4  SF4 B 603 " - pdb=" SG  CYS B 483 "
        pdb="FE2  SF4 B 603 " - pdb=" SG  CYS B 440 "
        pdb="FE1  SF4 B 603 " - pdb=" SG  CYS B 434 "
        pdb="FE3  SF4 B 603 " - pdb=" SG  CYS B 479 "
      Number of angles added : 12


  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2022

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 10 sheets defined
      42.5% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 90
      removed outlier: 3.638A  pdb=" N   VAL A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 109
      removed outlier: 5.357A  pdb=" N   ALA A 107 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 136
    Processing helix  chain 'A' and resid 162 through 175
    Processing helix  chain 'A' and resid 190 through 204
      removed outlier: 3.626A  pdb=" N   ALA A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ARG A 200 " --> pdb=" O   GLU A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 267
      removed outlier: 4.358A  pdb=" N   GLY A 267 " --> pdb=" O   GLY A 264 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 264 through 267'
    Processing helix  chain 'A' and resid 283 through 294
    Processing helix  chain 'A' and resid 311 through 318
    Processing helix  chain 'A' and resid 325 through 335
    Processing helix  chain 'A' and resid 341 through 345
    Processing helix  chain 'A' and resid 347 through 358
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 372 through 380
    Processing helix  chain 'A' and resid 393 through 398
    Processing helix  chain 'A' and resid 419 through 427
      removed outlier: 3.575A  pdb=" N   SER A 423 " --> pdb=" O   GLY A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 463
      removed outlier: 3.578A  pdb=" N   GLY A 463 " --> pdb=" O   PRO A 460 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 460 through 463'
    Processing helix  chain 'A' and resid 464 through 478
    Processing helix  chain 'A' and resid 491 through 496
      removed outlier: 3.814A  pdb=" N   PHE A 496 " --> pdb=" O   PHE A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 508
    Processing helix  chain 'A' and resid 527 through 535
      removed outlier: 3.568A  pdb=" N   LYS A 531 " --> pdb=" O   TYR A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 545
    Processing helix  chain 'A' and resid 557 through 574
    Processing helix  chain 'A' and resid 577 through 591
    Processing helix  chain 'B' and resid 16 through 25
    Processing helix  chain 'B' and resid 31 through 36
    Processing helix  chain 'B' and resid 47 through 55
      removed outlier: 4.854A  pdb=" N   ARG B  53 " --> pdb=" O   PHE B  49 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   PHE B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   HIS B  55 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 72
    Processing helix  chain 'B' and resid 86 through 88
      No H-bonds generated for 'chain 'B' and resid 86 through 88'
    Processing helix  chain 'B' and resid 93 through 106
    Processing helix  chain 'B' and resid 126 through 128
      No H-bonds generated for 'chain 'B' and resid 126 through 128'
    Processing helix  chain 'B' and resid 129 through 140
      removed outlier: 3.807A  pdb=" N   HIS B 134 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 181
    Processing helix  chain 'B' and resid 186 through 192
    Processing helix  chain 'B' and resid 229 through 233
      removed outlier: 3.517A  pdb=" N   ASN B 233 " --> pdb=" O   LEU B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 281 through 297
    Processing helix  chain 'B' and resid 306 through 315
    Processing helix  chain 'B' and resid 315 through 328
    Processing helix  chain 'B' and resid 362 through 364
      No H-bonds generated for 'chain 'B' and resid 362 through 364'
    Processing helix  chain 'B' and resid 375 through 386
    Processing helix  chain 'B' and resid 404 through 418
      removed outlier: 4.245A  pdb=" N   ALA B 409 " --> pdb=" O   GLU B 405 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   LYS B 410 " --> pdb=" O   SER B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 425 through 430
      removed outlier: 3.504A  pdb=" N   GLU B 429 " --> pdb=" O   THR B 425 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASN B 430 " --> pdb=" O   PRO B 426 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 425 through 430'
    Processing helix  chain 'B' and resid 450 through 465
    Processing helix  chain 'B' and resid 485 through 489
      removed outlier: 3.690A  pdb=" N   ALA B 489 " --> pdb=" O   ALA B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 542
      removed outlier: 3.791A  pdb=" N   LYS B 540 " --> pdb=" O   GLY B 536 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG B 542 " --> pdb=" O   TRP B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 555
    Processing helix  chain 'B' and resid 563 through 568
      removed outlier: 3.649A  pdb=" N   LEU B 568 " --> pdb=" O   PRO B 564 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 97
      removed outlier: 6.888A  pdb=" N   LEU A 112 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   PHE A 151 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   VAL A 114 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 8.723A  pdb=" N   VAL A 150 " --> pdb=" O   LEU A 180 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   ASP A 182 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
      removed outlier: 8.090A  pdb=" N   SER A 152 " --> pdb=" O   ASP A 182 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   VAL A 184 " --> pdb=" O   SER A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 275 through 279
      removed outlier: 4.460A  pdb=" N   ARG A 436 " --> pdb=" O   TRP A 279 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   LEU A 241 " --> pdb=" O   ASP A 262 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   ASP A 262 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   ASP A 255 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 301 through 304
    Processing sheet with id=AA4, first strand: chain 'A' and resid 409 through 412
    Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 518
      removed outlier: 6.339A  pdb=" N   ASN A 483 " --> pdb=" O   ARG A 513 " (cutoff:3.500A)
      removed outlier: 8.052A  pdb=" N   ASP A 515 " --> pdb=" O   ASN A 483 " (cutoff:3.500A)
      removed outlier: 6.381A  pdb=" N   LEU A 485 " --> pdb=" O   ASP A 515 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ALA A 517 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   PHE A 487 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   ILE A 549 " --> pdb=" O   GLN A 595 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ASP A 597 " --> pdb=" O   ILE A 549 " (cutoff:3.500A)
      removed outlier: 6.671A  pdb=" N   VAL A 551 " --> pdb=" O   ASP A 597 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   TYR A 599 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 6.301A  pdb=" N   GLY A 553 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 57 through 60
      removed outlier: 6.670A  pdb=" N   LEU B  82 " --> pdb=" O   HIS B 123 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   HIS B 123 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92
      removed outlier: 3.846A  pdb=" N   ASP B 389 " --> pdb=" O   ALA B 401 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY B 402 " --> pdb=" O   TRP B 356 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   TRP B 356 " --> pdb=" O   GLY B 402 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 156 through 157
      removed outlier: 6.335A  pdb=" N   LEU B 156 " --> pdb=" O   VAL B 220 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   THR B 219 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 7.314A  pdb=" N   ALA B 239 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL B 221 " --> pdb=" O   ALA B 239 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   ALA B 241 " --> pdb=" O   VAL B 221 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   GLU B 242 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   LEU B 246 " --> pdb=" O   GLU B 242 " (cutoff:3.500A)
      removed outlier: 8.109A  pdb=" N   VAL B 247 " --> pdb=" O   PRO B 278 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   PHE B 249 " --> pdb=" O   TYR B 276 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   TYR B 276 " --> pdb=" O   PHE B 249 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   LEU B 251 " --> pdb=" O   PHE B 274 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 369 through 370
    Processing sheet with id=AB1, first strand: chain 'B' and resid 431 through 433
      removed outlier: 6.696A  pdb=" N   MET B 432 " --> pdb=" O   VAL B 476 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   ARG B 500 " --> pdb=" O   LYS B 496 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   TYR B 501 " --> pdb=" O   ASN B 521 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   LEU B 505 " --> pdb=" O   MET B 517 " (cutoff:3.500A)
      removed outlier: 5.027A  pdb=" N   MET B 517 " --> pdb=" O   LEU B 505 " (cutoff:3.500A)

    355 hydrogen bonds defined for protein.
    1006 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: 3.01

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.43: 3816
        1.43 -     1.64: 5102
        1.64 -     1.86: 46
        1.86 -     2.07: 4
        2.07 -     2.28: 12
  Bond restraints: 8980
  Sorted by residual:
  bond pdb=" O3P FAD A 600 "
       pdb=" P   FAD A 600 "
    ideal  model  delta    sigma   weight residual
    1.660  1.578  0.082 2.00e-02 2.50e+03 1.68e+01
  bond pdb=" O5B FAD A 600 "
       pdb=" PA  FAD A 600 "
    ideal  model  delta    sigma   weight residual
    1.634  1.567  0.067 2.00e-02 2.50e+03 1.13e+01
  bond pdb=" O5' FAD A 600 "
       pdb=" P   FAD A 600 "
    ideal  model  delta    sigma   weight residual
    1.637  1.571  0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" O3  PO4 B 601 "
       pdb=" P   PO4 B 601 "
    ideal  model  delta    sigma   weight residual
    1.569  1.504  0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" O4  PO4 B 601 "
       pdb=" P   PO4 B 601 "
    ideal  model  delta    sigma   weight residual
    1.568  1.505  0.063 2.00e-02 2.50e+03 9.82e+00
  ... (remaining 8975 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 11956
        1.91 -     3.81: 185
        3.81 -     5.72: 44
        5.72 -     7.63: 16
        7.63 -     9.53: 6
  Bond angle restraints: 12207
  Sorted by residual:
  angle pdb=" C   SER B 436 "
        pdb=" CA  SER B 436 "
        pdb=" CB  SER B 436 "
      ideal   model   delta    sigma   weight residual
     116.54  110.42    6.12 1.15e+00 7.56e-01 2.83e+01
  angle pdb=" C   LYS A  90 "
        pdb=" N   LEU A  91 "
        pdb=" CA  LEU A  91 "
      ideal   model   delta    sigma   weight residual
     121.54  129.37   -7.83 1.91e+00 2.74e-01 1.68e+01
  angle pdb=" CA  SER B 436 "
        pdb=" C   SER B 436 "
        pdb=" N   PHE B 437 "
      ideal   model   delta    sigma   weight residual
     119.52  116.86    2.66 7.90e-01 1.60e+00 1.13e+01
  angle pdb=" CA  GLU A 330 "
        pdb=" CB  GLU A 330 "
        pdb=" CG  GLU A 330 "
      ideal   model   delta    sigma   weight residual
     114.10  120.55   -6.45 2.00e+00 2.50e-01 1.04e+01
  angle pdb=" C2B SRM B 604 "
        pdb=" C3B SRM B 604 "
        pdb=" C4B SRM B 604 "
      ideal   model   delta    sigma   weight residual
     108.00   98.47    9.53 3.00e+00 1.11e-01 1.01e+01
  ... (remaining 12202 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.18: 4996
       28.18 -    56.36: 363
       56.36 -    84.53: 34
       84.53 -   112.71: 2
      112.71 -   140.89: 1
  Dihedral angle restraints: 5396
    sinusoidal: 2251
      harmonic: 3145
  Sorted by residual:
  dihedral pdb=" C3B SRM B 604 "
           pdb=" C2B SRM B 604 "
           pdb=" CDB SRM B 604 "
           pdb=" CEB SRM B 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -54.26   86.63 -140.89     1      2.00e+01 2.50e-03 4.26e+01
  dihedral pdb=" CA  ASN B 149 "
           pdb=" C   ASN B 149 "
           pdb=" N   ASP B 150 "
           pdb=" CA  ASP B 150 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.53  -16.47     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  ASP B 202 "
           pdb=" CB  ASP B 202 "
           pdb=" CG  ASP B 202 "
           pdb=" OD1 ASP B 202 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.61   56.61     1      2.00e+01 2.50e-03 1.08e+01
  ... (remaining 5393 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 856
       0.035 -    0.070: 324
       0.070 -    0.105: 103
       0.105 -    0.140: 38
       0.140 -    0.175: 4
  Chirality restraints: 1325
  Sorted by residual:
  chirality pdb=" CB  ILE B 206 "
            pdb=" CA  ILE B 206 "
            pdb=" CG1 ILE B 206 "
            pdb=" CG2 ILE B 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.66e-01
  chirality pdb=" CB  THR A 162 "
            pdb=" CA  THR A 162 "
            pdb=" OG1 THR A 162 "
            pdb=" CG2 THR A 162 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.16 2.00e-01 2.50e+01 6.77e-01
  chirality pdb=" C2A SRM B 604 "
            pdb=" C1A SRM B 604 "
            pdb=" CDA SRM B 604 "
            pdb=" CMA SRM B 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.63    2.48    0.15 2.00e-01 2.50e+01 5.59e-01
  ... (remaining 1322 not shown)

  Planarity restraints: 1589
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 335 "    0.034 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO B 336 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO B 336 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 336 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" NB  SRM B 604 "   -0.002 2.00e-02 2.50e+03   1.51e-02 2.84e+00
        pdb=" C1B SRM B 604 "   -0.011 2.00e-02 2.50e+03
        pdb=" C2B SRM B 604 "    0.015 2.00e-02 2.50e+03
        pdb=" C4A SRM B 604 "    0.019 2.00e-02 2.50e+03
        pdb=" CHB SRM B 604 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 131 "    0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO B 132 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO B 132 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 132 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1586 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.78: 1956
        2.78 -     3.37: 9633
        3.37 -     3.96: 17728
        3.96 -     4.55: 25236
        4.55 -     5.14: 37320
  Nonbonded interactions: 91873
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 270 "
            pdb=" O   GLU A 400 "
     model   vdw
     2.194 3.040
  nonbonded pdb=" O   GLU B 287 "
            pdb=" OG1 THR B 291 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" O   GLU A 109 "
            pdb=" OG1 THR A 146 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" OG  SER A 252 "
            pdb=" OD1 ASP A 495 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   GLY A 463 "
            pdb=" OG  SER A 552 "
     model   vdw
     2.256 3.040
  ... (remaining 91868 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.18 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     28.970
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.050
  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:14.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: -0.0042
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      :  0.004   0.082   8980  Z= 0.263
  Angle     :  0.664   9.532  12207  Z= 0.313
  Chirality :  0.043   0.175   1325
  Planarity :  0.004   0.051   1589
  Dihedral  : 18.108 140.888   3374
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  3.51 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 27.80 %
    Favored  : 69.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.30 (0.26), residues: 1086
  helix:  1.40 (0.28), residues: 389
  sheet: -0.34 (0.37), residues: 203
  loop : -0.46 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 295 
 HIS   0.002   0.001   HIS B  55 
 PHE   0.016   0.002   PHE A 103 
 TYR   0.019   0.001   TYR A 332 
 ARG   0.005   0.000   ARG B  29 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  543 ILE cc_start: -0.0194 (mt) cc_final: -0.1597 (mm)
REVERT: A  592 ARG cc_start: 0.0616 (mmm160) cc_final: -0.1205 (ttm170)
REVERT: B  135 GLN cc_start: 0.0618 (mm110) cc_final: -0.0438 (pt0)
REVERT: B  136 MET cc_start: 0.2872 (pp-130) cc_final: 0.1155 (mmm)
REVERT: B  192 TRP cc_start: 0.0643 (m100) cc_final: 0.0288 (m100)
REVERT: B  439 THR cc_start: -0.0495 (OUTLIER) cc_final: -0.0715 (p)
  outliers start: 24
  outliers final: 5
  residues processed: 86
  average time/residue: 0.8645
  time to fit residues: 82.2983
Evaluate side-chains
  52 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain B residue   93 THR
Chi-restraints excluded: chain B residue  107 THR
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  439 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    5.9990
   chunk 84 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9990
   chunk 51 optimal weight:   40.0000
   chunk 63 optimal weight:    0.3980
   chunk 98 optimal weight:   20.0000
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
A 132 HIS
** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5014 r_free = 0.5014 target = 0.293841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.213813 restraints weight = 20215.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.4234 rms_B_bonded: 5.79
r_work: 0.3965 rms_B_bonded: 5.70 restraints_weight: 2.0000
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3948
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3948 r_free = 0.3948    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3948 r_free = 0.3948    target_work(ls_wunit_k1) = 0.171         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3948
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0173
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8980  Z= 0.269
  Angle     :  0.784  10.965  12207  Z= 0.383
  Chirality :  0.046   0.203   1325
  Planarity :  0.006   0.053   1589
  Dihedral  :  7.736 139.158   1279
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.44 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 25.38 %
    Favored  : 69.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.10 (0.25), residues: 1086
  helix:  1.22 (0.27), residues: 391
  sheet: -0.35 (0.36), residues: 188
  loop : -0.63 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 542 
 HIS   0.010   0.001   HIS B  55 
 PHE   0.022   0.003   PHE B 122 
 TYR   0.020   0.002   TYR A 527 
 ARG   0.010   0.001   ARG A 596 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 46
  time to evaluate  : 0.812 
Fit side-chains
REVERT: A  104 LYS cc_start: 0.0212 (OUTLIER) cc_final: -0.0203 (mtpt)
REVERT: A  545 ASP cc_start: 0.1869 (m-30) cc_final: 0.1424 (t0)
REVERT: A  582 ASP cc_start: 0.1809 (t0) cc_final: 0.1608 (t70)
REVERT: A  591 GLU cc_start: -0.0634 (OUTLIER) cc_final: -0.1061 (tp30)
REVERT: A  592 ARG cc_start: -0.0396 (mmm160) cc_final: -0.2026 (mtt90)
REVERT: B  126 LEU cc_start: 0.0039 (OUTLIER) cc_final: -0.0369 (mm)
REVERT: B  135 GLN cc_start: -0.1246 (mm110) cc_final: -0.1942 (pt0)
REVERT: B  136 MET cc_start: 0.2927 (OUTLIER) cc_final: 0.0728 (mmm)
REVERT: B  413 LYS cc_start: 0.2911 (OUTLIER) cc_final: 0.2381 (mmtt)
REVERT: B  432 MET cc_start: 0.2510 (mtt) cc_final: 0.1979 (mtm)
REVERT: B  485 ARG cc_start: 0.0031 (mtm-85) cc_final: -0.1274 (mtt180)
REVERT: B  533 GLU cc_start: 0.2603 (OUTLIER) cc_final: 0.2136 (tp30)
  outliers start: 46
  outliers final: 12
  residues processed: 87
  average time/residue: 0.9663
  time to fit residues: 91.8985
Evaluate side-chains
  59 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 LYS
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  458 ILE
Chi-restraints excluded: chain B residue  533 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 16 optimal weight:   30.0000
   chunk 12 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 29 optimal weight:    6.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
B  59 GLN
B  78 HIS
** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 250 ASN
B 395 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5020 r_free = 0.5020 target = 0.295833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.244808 restraints weight = 24489.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.4612 rms_B_bonded: 3.96
r_work (final): 0.4612
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4613
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4613 r_free = 0.4613    target_work(ls_wunit_k1) = 0.243         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4612 r_free = 0.4612    target_work(ls_wunit_k1) = 0.243         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0763
moved from start:          0.4402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   8980  Z= 0.287
  Angle     :  0.812  11.489  12207  Z= 0.396
  Chirality :  0.047   0.173   1325
  Planarity :  0.007   0.060   1589
  Dihedral  :  8.013 137.665   1272
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.81 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  5.38 %
    Allowed  : 24.07 %
    Favored  : 70.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.27 (0.25), residues: 1086
  helix:  0.84 (0.27), residues: 389
  sheet: -0.30 (0.38), residues: 182
  loop : -0.88 (0.27), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 484 
 HIS   0.005   0.001   HIS B 138 
 PHE   0.027   0.003   PHE A 161 
 TYR   0.022   0.002   TYR B  27 
 ARG   0.005   0.001   ARG B  29 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 47
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: 0.3662 (tt0) cc_final: 0.2997 (mt-10)
REVERT: A  127 GLU cc_start: 0.0547 (OUTLIER) cc_final: -0.0805 (pm20)
REVERT: A  174 GLU cc_start: 0.0004 (OUTLIER) cc_final: -0.0465 (tp30)
REVERT: A  379 LEU cc_start: 0.0839 (OUTLIER) cc_final: 0.0605 (mm)
REVERT: A  444 ASN cc_start: 0.1302 (OUTLIER) cc_final: -0.0969 (p0)
REVERT: A  532 LEU cc_start: 0.0566 (OUTLIER) cc_final: -0.0242 (mt)
REVERT: A  591 GLU cc_start: 0.0574 (OUTLIER) cc_final: 0.0364 (mt-10)
REVERT: B  125 ILE cc_start: -0.2724 (OUTLIER) cc_final: -0.4370 (pt)
REVERT: B  136 MET cc_start: 0.3585 (OUTLIER) cc_final: 0.1360 (mmm)
REVERT: B  186 ARG cc_start: 0.1645 (mtt90) cc_final: 0.1281 (mmm160)
REVERT: B  192 TRP cc_start: 0.2220 (m100) cc_final: 0.1156 (m100)
REVERT: B  203 GLU cc_start: 0.2310 (OUTLIER) cc_final: 0.0254 (mt-10)
REVERT: B  211 TYR cc_start: 0.0487 (m-80) cc_final: 0.0279 (t80)
REVERT: B  413 LYS cc_start: 0.2841 (OUTLIER) cc_final: 0.2204 (mmtt)
REVERT: B  462 MET cc_start: 0.2971 (tpp) cc_final: -0.0165 (pmm)
REVERT: B  487 MET cc_start: 0.3261 (mpp) cc_final: 0.2459 (mmm)
  outliers start: 49
  outliers final: 21
  residues processed: 88
  average time/residue: 1.0097
  time to fit residues: 96.7741
Evaluate side-chains
  72 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 41
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain A residue  591 GLU
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0030
   chunk 54 optimal weight:    0.0870
   chunk 23 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 4 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 101 optimal weight:    9.9990
   chunk 76 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0980
   overall best weight:    0.5570

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

Flipped N/Q/H residues before XYZ refinement:
B 106 ASN
B 129 ASN
B 195 GLN
B 236 ASN
B 504 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5076 r_free = 0.5076 target = 0.302549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.228275 restraints weight = 17576.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.4411 rms_B_bonded: 4.43
r_work: 0.4223 rms_B_bonded: 4.70 restraints_weight: 0.5000
r_work (final): 0.4223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4235 r_free = 0.4235    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4235 r_free = 0.4235    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0294
moved from start:          0.4675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8980  Z= 0.188
  Angle     :  0.671  11.398  12207  Z= 0.319
  Chirality :  0.043   0.140   1325
  Planarity :  0.005   0.059   1589
  Dihedral  :  7.697 142.826   1272
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.16 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 25.49 %
    Favored  : 70.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.01 (0.26), residues: 1086
  helix:  1.16 (0.27), residues: 392
  sheet: -0.28 (0.38), residues: 182
  loop : -0.75 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 484 
 HIS   0.008   0.001   HIS B 134 
 PHE   0.021   0.002   PHE B  49 
 TYR   0.018   0.001   TYR B  27 
 ARG   0.003   0.000   ARG A 520 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 46
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 PHE cc_start: 0.3470 (t80) cc_final: 0.3253 (t80)
REVERT: A  532 LEU cc_start: -0.0629 (OUTLIER) cc_final: -0.1078 (mt)
REVERT: A  582 ASP cc_start: 0.0997 (t0) cc_final: 0.0532 (t70)
REVERT: A  592 ARG cc_start: -0.0605 (mmm160) cc_final: -0.2081 (ttm170)
REVERT: B   36 LEU cc_start: -0.2069 (OUTLIER) cc_final: -0.2672 (mt)
REVERT: B   37 ASN cc_start: 0.3431 (m-40) cc_final: 0.2542 (t0)
REVERT: B  125 ILE cc_start: -0.4763 (OUTLIER) cc_final: -0.5578 (pt)
REVERT: B  136 MET cc_start: 0.2986 (pp-130) cc_final: 0.0856 (mmm)
REVERT: B  192 TRP cc_start: -0.0042 (m100) cc_final: -0.0439 (m100)
REVERT: B  370 TYR cc_start: 0.2795 (OUTLIER) cc_final: 0.1955 (t80)
REVERT: B  413 LYS cc_start: 0.2980 (OUTLIER) cc_final: 0.2361 (mmtt)
REVERT: B  462 MET cc_start: 0.2856 (OUTLIER) cc_final: -0.0368 (pmm)
REVERT: B  485 ARG cc_start: 0.0459 (mtm180) cc_final: 0.0033 (mtt180)
REVERT: B  487 MET cc_start: 0.3326 (mpp) cc_final: 0.3006 (mtm)
REVERT: B  533 GLU cc_start: 0.2983 (OUTLIER) cc_final: 0.2294 (tp30)
  outliers start: 33
  outliers final: 16
  residues processed: 72
  average time/residue: 0.9677
  time to fit residues: 76.4450
Evaluate side-chains
  63 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 40
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  155 ASP
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  533 GLU
Chi-restraints excluded: chain B residue  546 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 82 optimal weight:    5.9990
   chunk 20 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 32 optimal weight:    7.9990
   chunk 90 optimal weight:    0.0770
   chunk 86 optimal weight:    2.9990
   chunk 12 optimal weight:    0.1980
   chunk 45 optimal weight:    1.9990
   chunk 75 optimal weight:    9.9990
   chunk 101 optimal weight:   20.0000
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.4544

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

Flipped N/Q/H residues before XYZ refinement:
** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 195 GLN
B 396 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5091 r_free = 0.5091 target = 0.304790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4741 r_free = 0.4741 target = 0.254937 restraints weight = 24144.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.4680 rms_B_bonded: 3.93
r_work (final): 0.4680
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4688 r_free = 0.4688    target_work(ls_wunit_k1) = 0.252         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4688 r_free = 0.4688    target_work(ls_wunit_k1) = 0.252         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0819
moved from start:          0.5396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8980  Z= 0.265
  Angle     :  0.771  11.359  12207  Z= 0.373
  Chirality :  0.045   0.157   1325
  Planarity :  0.006   0.058   1589
  Dihedral  :  7.771 141.017   1272
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.71 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 24.84 %
    Favored  : 70.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.29 (0.25), residues: 1086
  helix:  0.86 (0.27), residues: 391
  sheet: -0.32 (0.39), residues: 176
  loop : -0.92 (0.27), residues: 519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 484 
 HIS   0.008   0.001   HIS B 123 
 PHE   0.024   0.003   PHE A 486 
 TYR   0.028   0.002   TYR B  27 
 ARG   0.008   0.001   ARG B  77 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 45
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: -0.0549 (mt-10) cc_final: -0.1121 (mm-30)
REVERT: A  174 GLU cc_start: 0.0226 (OUTLIER) cc_final: -0.0377 (tp30)
REVERT: A  457 MET cc_start: 0.1914 (mpt) cc_final: 0.1663 (mpt)
REVERT: B   36 LEU cc_start: 0.0178 (OUTLIER) cc_final: -0.0230 (tp)
REVERT: B  125 ILE cc_start: -0.2938 (OUTLIER) cc_final: -0.4440 (pt)
REVERT: B  136 MET cc_start: 0.3808 (OUTLIER) cc_final: 0.1346 (mmm)
REVERT: B  209 GLN cc_start: -0.1155 (OUTLIER) cc_final: -0.1778 (mp-120)
REVERT: B  370 TYR cc_start: 0.3149 (OUTLIER) cc_final: 0.2349 (t80)
REVERT: B  373 ARG cc_start: -0.0663 (OUTLIER) cc_final: -0.1081 (ttm110)
REVERT: B  375 LEU cc_start: -0.0528 (OUTLIER) cc_final: -0.1374 (mt)
REVERT: B  413 LYS cc_start: 0.2846 (OUTLIER) cc_final: 0.2206 (mmtt)
REVERT: B  462 MET cc_start: 0.3151 (OUTLIER) cc_final: -0.0051 (pmm)
REVERT: B  487 MET cc_start: 0.2824 (mpp) cc_final: 0.2324 (mtm)
REVERT: B  533 GLU cc_start: 0.3384 (OUTLIER) cc_final: 0.2616 (tp30)
  outliers start: 44
  outliers final: 23
  residues processed: 77
  average time/residue: 1.1151
  time to fit residues: 93.2882
Evaluate side-chains
  75 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 41
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  576 MET
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   36 LEU
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  373 ARG
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  533 GLU
Chi-restraints excluded: chain B residue  546 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 22 optimal weight:   10.0000
   chunk 102 optimal weight:   20.0000
   chunk 72 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 79 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 76 optimal weight:    6.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5106 r_free = 0.5106 target = 0.306378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.240537 restraints weight = 28948.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.4522 rms_B_bonded: 8.24
r_work: 0.4215 rms_B_bonded: 5.77 restraints_weight: 2.0000
r_work (final): 0.4215
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4235 r_free = 0.4235    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4235 r_free = 0.4235    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0316
moved from start:          0.5597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8980  Z= 0.199
  Angle     :  0.679  10.117  12207  Z= 0.322
  Chirality :  0.043   0.156   1325
  Planarity :  0.005   0.060   1589
  Dihedral  :  7.605 146.904   1272
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.44 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 24.95 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.16 (0.26), residues: 1086
  helix:  0.99 (0.27), residues: 392
  sheet: -0.34 (0.38), residues: 194
  loop : -0.84 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 484 
 HIS   0.007   0.001   HIS B 134 
 PHE   0.018   0.002   PHE A 161 
 TYR   0.018   0.001   TYR B  27 
 ARG   0.004   0.000   ARG B 345 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 42
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: -0.0467 (mt-10) cc_final: -0.1277 (mm-30)
REVERT: A  444 ASN cc_start: 0.0476 (OUTLIER) cc_final: -0.1423 (p0)
REVERT: A  485 LEU cc_start: 0.2721 (tp) cc_final: 0.1972 (mt)
REVERT: A  558 MET cc_start: 0.0519 (OUTLIER) cc_final: -0.0459 (tpp)
REVERT: B   37 ASN cc_start: 0.3623 (m-40) cc_final: 0.2803 (t0)
REVERT: B  136 MET cc_start: 0.2994 (OUTLIER) cc_final: 0.0788 (mmm)
REVERT: B  209 GLN cc_start: -0.2723 (OUTLIER) cc_final: -0.3209 (mp10)
REVERT: B  370 TYR cc_start: 0.2386 (OUTLIER) cc_final: 0.1428 (t80)
REVERT: B  375 LEU cc_start: -0.1702 (OUTLIER) cc_final: -0.2178 (mt)
REVERT: B  413 LYS cc_start: 0.2938 (OUTLIER) cc_final: 0.2384 (mmtt)
REVERT: B  462 MET cc_start: 0.3084 (OUTLIER) cc_final: -0.0166 (pmm)
REVERT: B  487 MET cc_start: 0.3351 (mpp) cc_final: 0.3018 (mtm)
REVERT: B  533 GLU cc_start: 0.3129 (OUTLIER) cc_final: 0.2337 (tp30)
  outliers start: 45
  outliers final: 27
  residues processed: 76
  average time/residue: 0.9573
  time to fit residues: 80.0934
Evaluate side-chains
  77 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 41
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  115 VAL
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  558 MET
Chi-restraints excluded: chain A residue  590 VAL
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   57 MET
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   73 LYS
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  150 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  533 GLU
Chi-restraints excluded: chain B residue  546 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 50 optimal weight:    0.0980
   chunk 51 optimal weight:    0.0170
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0980
   chunk 45 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 102 optimal weight:    8.9990
   chunk 52 optimal weight:    9.9990
   chunk 18 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.3418

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5114 r_free = 0.5114 target = 0.307478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.4605 r_free = 0.4605 target = 0.242761 restraints weight = 26887.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.4539 rms_B_bonded: 7.32
r_work: 0.4242 rms_B_bonded: 5.52 restraints_weight: 2.0000
r_work (final): 0.4242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4269
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4269 r_free = 0.4269    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4269 r_free = 0.4269    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4269
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0286
moved from start:          0.5680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8980  Z= 0.164
  Angle     :  0.631  10.526  12207  Z= 0.296
  Chirality :  0.042   0.174   1325
  Planarity :  0.005   0.060   1589
  Dihedral  :  7.412 148.158   1272
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.44 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 25.82 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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:  0.10 (0.26), residues: 1086
  helix:  1.23 (0.27), residues: 394
  sheet: -0.35 (0.38), residues: 201
  loop : -0.65 (0.28), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 197 
 HIS   0.007   0.001   HIS B 134 
 PHE   0.014   0.001   PHE A 161 
 TYR   0.012   0.001   TYR B  27 
 ARG   0.002   0.000   ARG B  69 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 39
  time to evaluate  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: -0.0505 (mt-10) cc_final: -0.1250 (mm-30)
REVERT: A  558 MET cc_start: 0.0560 (OUTLIER) cc_final: -0.0404 (tpp)
REVERT: B   37 ASN cc_start: 0.3481 (m-40) cc_final: 0.2825 (t0)
REVERT: B  136 MET cc_start: 0.3012 (OUTLIER) cc_final: 0.0880 (mmm)
REVERT: B  196 GLU cc_start: -0.0118 (OUTLIER) cc_final: -0.0711 (mt-10)
REVERT: B  211 TYR cc_start: 0.0830 (m-80) cc_final: 0.0404 (t80)
REVERT: B  370 TYR cc_start: 0.2586 (OUTLIER) cc_final: 0.1446 (t80)
REVERT: B  413 LYS cc_start: 0.2813 (OUTLIER) cc_final: 0.2298 (mmtt)
REVERT: B  462 MET cc_start: 0.3045 (OUTLIER) cc_final: -0.0181 (pmm)
REVERT: B  487 MET cc_start: 0.3280 (mpp) cc_final: 0.2998 (mtm)
  outliers start: 37
  outliers final: 21
  residues processed: 65
  average time/residue: 1.1244
  time to fit residues: 79.7862
Evaluate side-chains
  65 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 38
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  558 MET
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   57 MET
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   73 LYS
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  279 LEU
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  546 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 99 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0060
   chunk 104 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    0.9798

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN
B 281 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5123 r_free = 0.5123 target = 0.308561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.243068 restraints weight = 19515.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.4510 rms_B_bonded: 4.90
r_work (final): 0.4510
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4533
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4533 r_free = 0.4533    target_work(ls_wunit_k1) = 0.232         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4533 r_free = 0.4533    target_work(ls_wunit_k1) = 0.232         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4533
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0399
moved from start:          0.6132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8980  Z= 0.209
  Angle     :  0.689  10.666  12207  Z= 0.329
  Chirality :  0.044   0.236   1325
  Planarity :  0.005   0.059   1589
  Dihedral  :  7.484 145.680   1272
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 13.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.90 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 26.04 %
    Favored  : 69.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.15 (0.26), residues: 1086
  helix:  1.01 (0.27), residues: 393
  sheet: -0.57 (0.38), residues: 192
  loop : -0.72 (0.28), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.007   0.001   HIS B 123 
 PHE   0.017   0.002   PHE A 161 
 TYR   0.018   0.001   TYR B  27 
 ARG   0.004   0.000   ARG B  63 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 39
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: -0.0288 (mt-10) cc_final: -0.1045 (mm-30)
REVERT: A  444 ASN cc_start: 0.0486 (OUTLIER) cc_final: -0.1359 (p0)
REVERT: A  558 MET cc_start: -0.0107 (OUTLIER) cc_final: -0.1214 (tpp)
REVERT: B  136 MET cc_start: 0.3225 (OUTLIER) cc_final: 0.0895 (mmm)
REVERT: B  196 GLU cc_start: -0.0302 (OUTLIER) cc_final: -0.0979 (mt-10)
REVERT: B  209 GLN cc_start: -0.2340 (OUTLIER) cc_final: -0.2725 (pm20)
REVERT: B  370 TYR cc_start: 0.2693 (OUTLIER) cc_final: 0.1567 (t80)
REVERT: B  375 LEU cc_start: -0.1917 (OUTLIER) cc_final: -0.2343 (mt)
REVERT: B  413 LYS cc_start: 0.2667 (OUTLIER) cc_final: 0.2173 (mmtt)
REVERT: B  462 MET cc_start: 0.3236 (OUTLIER) cc_final: 0.0102 (pmm)
REVERT: B  487 MET cc_start: 0.2932 (mpp) cc_final: 0.2467 (mtm)
  outliers start: 37
  outliers final: 26
  residues processed: 66
  average time/residue: 1.1694
  time to fit residues: 83.7813
Evaluate side-chains
  72 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 37
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  558 MET
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   57 MET
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   73 LYS
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  546 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    0.0770
   chunk 36 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 89 optimal weight:    9.9990
   chunk 0 optimal weight:    4.9990
   chunk 105 optimal weight:    8.9990
   chunk 75 optimal weight:    0.0170
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5129 r_free = 0.5129 target = 0.309839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.246204 restraints weight = 21769.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.4544 rms_B_bonded: 5.76
r_work: 0.4323 rms_B_bonded: 5.36 restraints_weight: 2.0000
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4321 r_free = 0.4321    target_work(ls_wunit_k1) = 0.208         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4321 r_free = 0.4321    target_work(ls_wunit_k1) = 0.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4321
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0368
moved from start:          0.6515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8980  Z= 0.210
  Angle     :  0.702  10.633  12207  Z= 0.336
  Chirality :  0.044   0.281   1325
  Planarity :  0.006   0.077   1589
  Dihedral  :  7.478 143.764   1272
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.73 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 26.48 %
    Favored  : 69.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.21 (0.26), residues: 1086
  helix:  0.96 (0.27), residues: 393
  sheet: -0.59 (0.38), residues: 195
  loop : -0.78 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 348 
 HIS   0.007   0.001   HIS B 123 
 PHE   0.019   0.002   PHE A 161 
 TYR   0.015   0.001   TYR B  27 
 ARG   0.010   0.000   ARG B  20 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 40
  time to evaluate  : 0.912 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 GLU cc_start: -0.0243 (mt-10) cc_final: -0.0622 (tp30)
REVERT: A  444 ASN cc_start: 0.0472 (OUTLIER) cc_final: -0.1454 (p0)
REVERT: A  532 LEU cc_start: 0.0049 (mp) cc_final: -0.0354 (mt)
REVERT: A  558 MET cc_start: 0.0395 (OUTLIER) cc_final: -0.1070 (tpp)
REVERT: B  136 MET cc_start: 0.3115 (OUTLIER) cc_final: 0.0806 (mmm)
REVERT: B  186 ARG cc_start: -0.0087 (mtt180) cc_final: -0.1339 (mmt180)
REVERT: B  370 TYR cc_start: 0.2851 (OUTLIER) cc_final: 0.1931 (t80)
REVERT: B  375 LEU cc_start: -0.2062 (OUTLIER) cc_final: -0.2262 (mt)
REVERT: B  413 LYS cc_start: 0.2655 (OUTLIER) cc_final: 0.2206 (ptpt)
REVERT: B  462 MET cc_start: 0.3156 (OUTLIER) cc_final: -0.0151 (pmm)
  outliers start: 38
  outliers final: 27
  residues processed: 67
  average time/residue: 1.1061
  time to fit residues: 81.3653
Evaluate side-chains
  71 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 37
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  558 MET
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   57 MET
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   73 LYS
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  195 GLN
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  375 LEU
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  546 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    0.2980
   chunk 69 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 16 optimal weight:   20.0000
   chunk 27 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 103 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0980
   chunk 36 optimal weight:    5.9990
   chunk 11 optimal weight:    0.8980
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 195 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5137 r_free = 0.5137 target = 0.311113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.259873 restraints weight = 28296.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.4726 rms_B_bonded: 4.32
r_work (final): 0.4726
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4733 r_free = 0.4733    target_work(ls_wunit_k1) = 0.256         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4733 r_free = 0.4733    target_work(ls_wunit_k1) = 0.256         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0716
moved from start:          0.6625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8980  Z= 0.176
  Angle     :  0.657  10.379  12207  Z= 0.310
  Chirality :  0.043   0.222   1325
  Planarity :  0.005   0.060   1589
  Dihedral  :  7.390 144.377   1272
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.08 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 27.03 %
    Favored  : 69.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.06 (0.26), residues: 1086
  helix:  1.10 (0.27), residues: 395
  sheet: -0.53 (0.38), residues: 191
  loop : -0.69 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.007   0.001   HIS B 123 
 PHE   0.017   0.001   PHE A 161 
 TYR   0.010   0.001   TYR B  27 
 ARG   0.009   0.000   ARG B  20 

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

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

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2172 Ramachandran restraints generated.
    1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 39
  time to evaluate  : 0.829 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.0607 (OUTLIER) cc_final: -0.1174 (p0)
REVERT: A  532 LEU cc_start: 0.0903 (mp) cc_final: 0.0087 (mt)
REVERT: A  558 MET cc_start: 0.0487 (OUTLIER) cc_final: -0.0479 (tpp)
REVERT: B   37 ASN cc_start: 0.4443 (m-40) cc_final: 0.3049 (t0)
REVERT: B  125 ILE cc_start: -0.3304 (OUTLIER) cc_final: -0.4003 (mt)
REVERT: B  136 MET cc_start: 0.3871 (OUTLIER) cc_final: 0.1248 (mmm)
REVERT: B  186 ARG cc_start: 0.0826 (mtt180) cc_final: -0.0330 (tpp-160)
REVERT: B  209 GLN cc_start: -0.0317 (OUTLIER) cc_final: -0.1474 (pm20)
REVERT: B  370 TYR cc_start: 0.3347 (OUTLIER) cc_final: 0.2181 (t80)
REVERT: B  413 LYS cc_start: 0.2411 (OUTLIER) cc_final: 0.1940 (ptpt)
REVERT: B  462 MET cc_start: 0.3361 (OUTLIER) cc_final: 0.0287 (pmm)
  outliers start: 33
  outliers final: 22
  residues processed: 61
  average time/residue: 1.0590
  time to fit residues: 70.6412
Evaluate side-chains
  67 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 37
  time to evaluate  : 0.946 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  135 LEU
Chi-restraints excluded: chain A residue  168 PHE
Chi-restraints excluded: chain A residue  184 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  308 THR
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  444 ASN
Chi-restraints excluded: chain A residue  558 MET
Chi-restraints excluded: chain B residue    4 LYS
Chi-restraints excluded: chain B residue    5 HIS
Chi-restraints excluded: chain B residue   57 MET
Chi-restraints excluded: chain B residue   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  125 ILE
Chi-restraints excluded: chain B residue  128 LYS
Chi-restraints excluded: chain B residue  136 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  185 THR
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  211 TYR
Chi-restraints excluded: chain B residue  370 TYR
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Chi-restraints excluded: chain B residue  546 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 28 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0060
   chunk 64 optimal weight:    0.4980
   chunk 19 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 31 optimal weight:   20.0000
   chunk 42 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   overall best weight:    1.0998

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

Flipped N/Q/H residues before XYZ refinement:
A 258 HIS
** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 397 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5144 r_free = 0.5144 target = 0.311420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4709 r_free = 0.4709 target = 0.253831 restraints weight = 21693.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.4655 rms_B_bonded: 5.84
r_work: 0.4428 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.4428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4423
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4423 r_free = 0.4423    target_work(ls_wunit_k1) = 0.219         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4423 r_free = 0.4423    target_work(ls_wunit_k1) = 0.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4423
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0430
moved from start:          0.7127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8980  Z= 0.224
  Angle     :  0.735  10.680  12207  Z= 0.354
  Chirality :  0.045   0.264   1325
  Planarity :  0.006   0.057   1589
  Dihedral  :  7.497 143.729   1272
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 14.94
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.18 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 27.03 %
    Favored  : 69.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.21 (0.26), residues: 1086
  helix:  0.91 (0.27), residues: 394
  sheet: -0.42 (0.39), residues: 181
  loop : -0.81 (0.27), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 540 
 HIS   0.010   0.001   HIS A 548 
 PHE   0.023   0.002   PHE A 161 
 TYR   0.014   0.001   TYR A 527 
 ARG   0.011   0.001   ARG B  20 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6640.42 seconds
wall clock time: 114 minutes 52.12 seconds (6892.12 seconds total)