Starting phenix.real_space_refine
on Mon May 12 07:21:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c91_45359/05_2025/9c91_45359.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c91_45359/05_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_45359/05_2025/9c91_45359.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c91_45359/05_2025/9c91_45359.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c91_45359/05_2025/9c91_45359.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c91_45359/05_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 7.33, per 1000 atoms: 0.83
  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.5 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: 1.01
  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: 2.47

  Time building geometry restraints manager: 2.72 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=" C4  FMN A 601 "
       pdb=" C4A FMN A 601 "
    ideal  model  delta    sigma   weight residual
    1.485  1.396  0.089 2.00e-02 2.50e+03 2.00e+01
  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=" C4A FMN A 601 "
       pdb=" N5  FMN A 601 "
    ideal  model  delta    sigma   weight residual
    1.300  1.379 -0.079 2.00e-02 2.50e+03 1.55e+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
  ... (remaining 8975 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 11936
        1.91 -     3.81: 197
        3.81 -     5.72: 48
        5.72 -     7.63: 19
        7.63 -     9.53: 7
  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: 4997
       28.18 -    56.36: 363
       56.36 -    84.53: 35
       84.53 -   112.71: 2
      112.71 -   140.89: 1
  Dihedral angle restraints: 5398
    sinusoidal: 2253
      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 5395 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 855
       0.035 -    0.070: 325
       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: 1590
  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 1587 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:             3.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.490
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.830
-------------------------------------------------------------------------------
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      :  0.005   0.089   8987  Z= 0.210
  Angle     :  0.757  19.584  12219  Z= 0.321
  Chirality :  0.043   0.175   1325
  Planarity :  0.004   0.051   1590
  Dihedral  : 18.115 140.888   3376
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16652 (  355)
  hydrogen bonds       : angle       6.99197 ( 1006)
  metal coordination   : bond        0.01592 (    4)
  metal coordination   : angle       9.90915 (   12)
  covalent geometry    : bond        0.00456 ( 8980)
  covalent geometry    : angle       0.69069 (12207)
  Misc. bond           : bond        0.02842 (    3)

*********************** 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  : 0.836 
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: 0.8554
  time to fit residues: 81.2167
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  : 0.944 
-------------------------------------------------------------------------------
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 = 0.5015 r_free = 0.5015 target = 0.294044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.211934 restraints weight = 20046.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.4230 rms_B_bonded: 5.62
r_work: 0.3998 rms_B_bonded: 5.40 restraints_weight: 2.0000
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3994 r_free = 0.3994    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3994 r_free = 0.3994    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0187
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8987  Z= 0.188
  Angle     :  0.870  18.599  12219  Z= 0.391
  Chirality :  0.047   0.203   1325
  Planarity :  0.006   0.053   1590
  Dihedral  :  7.612 139.200   1281
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.62 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 25.16 %
    Favored  : 69.67 %
  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:  0.05 (0.25), residues: 1086
  helix:  1.17 (0.27), residues: 391
  sheet: -0.36 (0.36), residues: 191
  loop : -0.66 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 542 
 HIS   0.010   0.001   HIS B  55 
 PHE   0.023   0.003   PHE B 122 
 TYR   0.020   0.002   TYR A 527 
 ARG   0.009   0.001   ARG A 596 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04110 (  355)
  hydrogen bonds       : angle       5.64872 ( 1006)
  metal coordination   : bond        0.01758 (    4)
  metal coordination   : angle      11.39388 (   12)
  covalent geometry    : bond        0.00415 ( 8980)
  covalent geometry    : angle       0.79380 (12207)
  Misc. bond           : bond        0.01282 (    3)

*********************** 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
  94 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 47
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A  104 LYS cc_start: 0.0218 (OUTLIER) cc_final: -0.0268 (mtpt)
REVERT: A  545 ASP cc_start: 0.1830 (m-30) cc_final: 0.1417 (t70)
REVERT: A  582 ASP cc_start: 0.2221 (t0) cc_final: 0.1961 (t70)
REVERT: A  591 GLU cc_start: -0.0637 (OUTLIER) cc_final: -0.1110 (tp30)
REVERT: A  592 ARG cc_start: -0.0438 (mmm160) cc_final: -0.2262 (mtt90)
REVERT: B  125 ILE cc_start: -0.4820 (OUTLIER) cc_final: -0.5593 (pp)
REVERT: B  126 LEU cc_start: -0.0087 (OUTLIER) cc_final: -0.0388 (mm)
REVERT: B  136 MET cc_start: 0.2905 (OUTLIER) cc_final: 0.0809 (mmm)
REVERT: B  413 LYS cc_start: 0.2943 (OUTLIER) cc_final: 0.2387 (mmtt)
REVERT: B  432 MET cc_start: 0.2866 (mtt) cc_final: 0.2658 (mmt)
REVERT: B  533 GLU cc_start: 0.2619 (OUTLIER) cc_final: 0.2131 (tp30)
  outliers start: 47
  outliers final: 14
  residues processed: 89
  average time/residue: 0.9154
  time to fit residues: 89.2001
Evaluate side-chains
  61 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 40
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
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  486 PHE
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  125 ILE
Chi-restraints excluded: chain B residue  126 LEU
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  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:    0.0040
   chunk 16 optimal weight:   30.0000
   chunk 12 optimal weight:    0.2980
   chunk 87 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 104 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.2598

-------------------------------------------------------------------------------
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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 395 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5020 r_free = 0.5020 target = 0.295259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4682 r_free = 0.4682 target = 0.247794 restraints weight = 24120.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.4645 rms_B_bonded: 3.98
r_work (final): 0.4645
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4658 r_free = 0.4658    target_work(ls_wunit_k1) = 0.248         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4657 r_free = 0.4657    target_work(ls_wunit_k1) = 0.248         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0725
moved from start:          0.3998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   8987  Z= 0.175
  Angle     :  0.845  25.650  12219  Z= 0.370
  Chirality :  0.045   0.163   1325
  Planarity :  0.006   0.053   1590
  Dihedral  :  7.585 137.520   1274
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.53 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 25.16 %
    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: -0.13 (0.26), residues: 1086
  helix:  0.99 (0.27), residues: 392
  sheet: -0.38 (0.38), residues: 182
  loop : -0.76 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 484 
 HIS   0.006   0.001   HIS B 134 
 PHE   0.039   0.003   PHE A 486 
 TYR   0.019   0.002   TYR B  27 
 ARG   0.005   0.001   ARG B 500 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03949 (  355)
  hydrogen bonds       : angle       5.48506 ( 1006)
  metal coordination   : bond        0.00960 (    4)
  metal coordination   : angle      11.37405 (   12)
  covalent geometry    : bond        0.00391 ( 8980)
  covalent geometry    : angle       0.76693 (12207)
  Misc. bond           : bond        0.02612 (    3)

*********************** 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
  80 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 41
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
REVERT: A  379 LEU cc_start: 0.0947 (OUTLIER) cc_final: 0.0699 (mm)
REVERT: A  532 LEU cc_start: 0.0153 (OUTLIER) cc_final: -0.0383 (mp)
REVERT: B  136 MET cc_start: 0.3270 (OUTLIER) cc_final: 0.1306 (mmm)
REVERT: B  192 TRP cc_start: 0.2116 (m100) cc_final: 0.1291 (m100)
REVERT: B  203 GLU cc_start: 0.2211 (OUTLIER) cc_final: 0.0329 (pt0)
REVERT: B  413 LYS cc_start: 0.2681 (OUTLIER) cc_final: 0.2140 (mmtt)
REVERT: B  487 MET cc_start: 0.3204 (mpp) cc_final: 0.2447 (mmm)
  outliers start: 39
  outliers final: 19
  residues processed: 73
  average time/residue: 0.9473
  time to fit residues: 75.9472
Evaluate side-chains
  62 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 38
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  155 ASP
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  486 PHE
Chi-restraints excluded: chain A residue  528 VAL
Chi-restraints excluded: chain A residue  532 LEU
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  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  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:   10.0000
   chunk 54 optimal weight:    0.0770
   chunk 23 optimal weight:    8.9990
   chunk 2 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 88 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9990
   chunk 101 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
B  78 HIS
** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 396 GLN
B 504 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5073 r_free = 0.5073 target = 0.301690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.229786 restraints weight = 16942.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.4412 rms_B_bonded: 4.20
r_work: 0.4207 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.4207
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4225
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4225 r_free = 0.4225    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4225 r_free = 0.4225    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4225
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0292
moved from start:          0.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8987  Z= 0.130
  Angle     :  0.771  24.165  12219  Z= 0.324
  Chirality :  0.044   0.339   1325
  Planarity :  0.005   0.057   1590
  Dihedral  :  7.489 143.899   1274
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.34 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 24.62 %
    Favored  : 71.21 %
  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:  0.03 (0.26), residues: 1086
  helix:  1.16 (0.27), residues: 393
  sheet: -0.35 (0.38), residues: 184
  loop : -0.70 (0.27), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 484 
 HIS   0.006   0.001   HIS B 134 
 PHE   0.018   0.002   PHE A 486 
 TYR   0.017   0.001   TYR B  27 
 ARG   0.003   0.000   ARG A 520 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03361 (  355)
  hydrogen bonds       : angle       5.10579 ( 1006)
  metal coordination   : bond        0.00754 (    4)
  metal coordination   : angle      11.54633 (   12)
  covalent geometry    : bond        0.00292 ( 8980)
  covalent geometry    : angle       0.68146 (12207)
  Misc. bond           : bond        0.01417 (    3)

*********************** 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: 38
    poor density    : 41
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.0681 (OUTLIER) cc_final: -0.0579 (p0)
REVERT: A  532 LEU cc_start: -0.0928 (OUTLIER) cc_final: -0.1454 (mt)
REVERT: A  582 ASP cc_start: 0.1450 (t0) cc_final: 0.1076 (t70)
REVERT: B   36 LEU cc_start: -0.2236 (OUTLIER) cc_final: -0.2591 (mp)
REVERT: B   37 ASN cc_start: 0.3411 (m-40) cc_final: 0.2511 (t0)
REVERT: B  136 MET cc_start: 0.3040 (OUTLIER) cc_final: 0.0831 (mmm)
REVERT: B  192 TRP cc_start: -0.0013 (m100) cc_final: -0.0427 (m100)
REVERT: B  413 LYS cc_start: 0.2862 (OUTLIER) cc_final: 0.2279 (mmtt)
REVERT: B  462 MET cc_start: 0.2927 (tpp) cc_final: -0.0338 (pmm)
REVERT: B  487 MET cc_start: 0.3401 (mpp) cc_final: 0.3115 (mtm)
REVERT: B  533 GLU cc_start: 0.2842 (OUTLIER) cc_final: 0.2234 (tp30)
  outliers start: 38
  outliers final: 18
  residues processed: 72
  average time/residue: 0.8144
  time to fit residues: 65.1811
Evaluate side-chains
  59 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 35
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  155 ASP
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  532 LEU
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  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  196 GLU
Chi-restraints excluded: chain B residue  221 VAL
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  533 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:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 90 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 101 optimal weight:   20.0000
   chunk 91 optimal weight:    4.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
B 236 ASN
B 250 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5090 r_free = 0.5090 target = 0.303948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.235242 restraints weight = 20935.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.4460 rms_B_bonded: 5.78
r_work: 0.4231 rms_B_bonded: 5.21 restraints_weight: 2.0000
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4228
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4228 r_free = 0.4228    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4228 r_free = 0.4228    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4228
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0324
moved from start:          0.5298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8987  Z= 0.154
  Angle     :  0.809  23.601  12219  Z= 0.348
  Chirality :  0.044   0.357   1325
  Planarity :  0.006   0.058   1590
  Dihedral  :  7.602 147.233   1274
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.90 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.84 %
    Favored  : 70.66 %
  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: -0.22 (0.25), residues: 1086
  helix:  0.98 (0.27), residues: 395
  sheet: -0.60 (0.38), residues: 173
  loop : -0.83 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 502 
 HIS   0.008   0.001   HIS B 123 
 PHE   0.018   0.002   PHE A 161 
 TYR   0.020   0.002   TYR B  27 
 ARG   0.005   0.001   ARG B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  355)
  hydrogen bonds       : angle       5.12964 ( 1006)
  metal coordination   : bond        0.00596 (    4)
  metal coordination   : angle      11.44368 (   12)
  covalent geometry    : bond        0.00345 ( 8980)
  covalent geometry    : angle       0.72598 (12207)
  Misc. bond           : bond        0.01381 (    3)

*********************** 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
  79 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 38
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 GLU cc_start: 0.0356 (OUTLIER) cc_final: -0.0435 (pm20)
REVERT: A  174 GLU cc_start: -0.1674 (OUTLIER) cc_final: -0.2298 (mp0)
REVERT: A  444 ASN cc_start: 0.0892 (OUTLIER) cc_final: -0.1661 (p0)
REVERT: A  532 LEU cc_start: -0.0616 (OUTLIER) cc_final: -0.0923 (mt)
REVERT: B  121 GLN cc_start: 0.2747 (OUTLIER) cc_final: 0.2366 (mt0)
REVERT: B  136 MET cc_start: 0.2863 (OUTLIER) cc_final: 0.0809 (mmm)
REVERT: B  209 GLN cc_start: -0.2052 (OUTLIER) cc_final: -0.2320 (mp10)
REVERT: B  413 LYS cc_start: 0.2800 (OUTLIER) cc_final: 0.2264 (mmtt)
REVERT: B  462 MET cc_start: 0.2964 (OUTLIER) cc_final: -0.0312 (pmm)
REVERT: B  487 MET cc_start: 0.3389 (mpp) cc_final: 0.3146 (mtm)
REVERT: B  533 GLU cc_start: 0.2905 (OUTLIER) cc_final: 0.2233 (tp30)
  outliers start: 41
  outliers final: 20
  residues processed: 70
  average time/residue: 0.9451
  time to fit residues: 72.8164
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  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
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  444 ASN
Chi-restraints excluded: chain A residue  532 LEU
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  121 GLN
Chi-restraints excluded: chain B residue  126 LEU
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  186 ARG
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  198 VAL
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  221 VAL
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
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:    8.9990
   chunk 102 optimal weight:    0.4980
   chunk 72 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 79 optimal weight:    6.9990
   chunk 9 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9990
   chunk 76 optimal weight:    8.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5121 r_free = 0.5121 target = 0.307806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4799 r_free = 0.4799 target = 0.261404 restraints weight = 28678.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.4730 rms_B_bonded: 4.40
r_work (final): 0.4730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4741
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4741 r_free = 0.4741    target_work(ls_wunit_k1) = 0.258         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4741 r_free = 0.4741    target_work(ls_wunit_k1) = 0.258         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4741
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0797
moved from start:          0.5699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8987  Z= 0.135
  Angle     :  0.781  23.673  12219  Z= 0.327
  Chirality :  0.044   0.256   1325
  Planarity :  0.005   0.061   1590
  Dihedral  :  7.379 142.531   1274
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.62 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 25.05 %
    Favored  : 70.77 %
  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: -0.14 (0.26), residues: 1086
  helix:  1.00 (0.27), residues: 396
  sheet: -0.46 (0.40), residues: 173
  loop : -0.77 (0.27), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 197 
 HIS   0.009   0.001   HIS B 123 
 PHE   0.018   0.002   PHE A 161 
 TYR   0.017   0.001   TYR B  27 
 ARG   0.005   0.000   ARG B 345 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03303 (  355)
  hydrogen bonds       : angle       4.93739 ( 1006)
  metal coordination   : bond        0.00659 (    4)
  metal coordination   : angle      11.81662 (   12)
  covalent geometry    : bond        0.00301 ( 8980)
  covalent geometry    : angle       0.68802 (12207)
  Misc. bond           : bond        0.01416 (    3)

*********************** 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
  78 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 40
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.0905 (OUTLIER) cc_final: -0.0811 (p0)
REVERT: A  471 MET cc_start: 0.3562 (tpp) cc_final: 0.3205 (tpp)
REVERT: A  486 PHE cc_start: 0.0668 (m-80) cc_final: 0.0222 (m-10)
REVERT: A  528 VAL cc_start: -0.0241 (OUTLIER) cc_final: -0.0681 (p)
REVERT: A  532 LEU cc_start: 0.0839 (OUTLIER) cc_final: 0.0017 (mt)
REVERT: A  558 MET cc_start: 0.0909 (OUTLIER) cc_final: -0.0022 (tpp)
REVERT: B   37 ASN cc_start: 0.4528 (m-40) cc_final: 0.3090 (t0)
REVERT: B  121 GLN cc_start: 0.3147 (OUTLIER) cc_final: 0.2904 (mt0)
REVERT: B  136 MET cc_start: 0.3634 (pp-130) cc_final: 0.1446 (mmm)
REVERT: B  209 GLN cc_start: -0.0406 (OUTLIER) cc_final: -0.1253 (mp10)
REVERT: B  375 LEU cc_start: -0.0592 (OUTLIER) cc_final: -0.1353 (mt)
REVERT: B  413 LYS cc_start: 0.2526 (OUTLIER) cc_final: 0.2048 (mmtt)
REVERT: B  462 MET cc_start: 0.3188 (OUTLIER) cc_final: 0.0144 (pmm)
REVERT: B  487 MET cc_start: 0.3056 (mpp) cc_final: 0.2519 (mtm)
REVERT: B  533 GLU cc_start: 0.3235 (OUTLIER) cc_final: 0.2530 (tp30)
  outliers start: 38
  outliers final: 16
  residues processed: 72
  average time/residue: 0.9337
  time to fit residues: 74.3204
Evaluate side-chains
  66 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 40
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
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  532 LEU
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   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  121 GLN
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  221 VAL
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  528 LEU
Chi-restraints excluded: chain B residue  533 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:    0.0670
   chunk 17 optimal weight:    4.9990
   chunk 7 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 102 optimal weight:    5.9990
   chunk 52 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.6920

-------------------------------------------------------------------------------
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 116 ASN ** 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 = 0.5117 r_free = 0.5117 target = 0.307777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.244184 restraints weight = 26978.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.4566 rms_B_bonded: 7.59
r_work: 0.4285 rms_B_bonded: 5.51 restraints_weight: 2.0000
r_work (final): 0.4285
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4283
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4283 r_free = 0.4283    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4283 r_free = 0.4283    target_work(ls_wunit_k1) = 0.204         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.4283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0330
moved from start:          0.6028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8987  Z= 0.128
  Angle     :  0.759  22.827  12219  Z= 0.318
  Chirality :  0.043   0.207   1325
  Planarity :  0.005   0.060   1590
  Dihedral  :  7.287 143.195   1274
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 13.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.44 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 25.93 %
    Favored  : 70.66 %
  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: -0.09 (0.26), residues: 1086
  helix:  1.05 (0.27), residues: 396
  sheet: -0.50 (0.38), residues: 183
  loop : -0.72 (0.27), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.008   0.001   HIS A 548 
 PHE   0.016   0.002   PHE A 161 
 TYR   0.017   0.001   TYR B 370 
 ARG   0.006   0.000   ARG B  77 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03154 (  355)
  hydrogen bonds       : angle       4.82853 ( 1006)
  metal coordination   : bond        0.00633 (    4)
  metal coordination   : angle      11.46532 (   12)
  covalent geometry    : bond        0.00285 ( 8980)
  covalent geometry    : angle       0.66904 (12207)
  Misc. bond           : bond        0.01329 (    3)

*********************** 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
  73 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 42
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.0706 (OUTLIER) cc_final: -0.1137 (p0)
REVERT: A  532 LEU cc_start: -0.0421 (OUTLIER) cc_final: -0.0925 (mp)
REVERT: A  539 LEU cc_start: -0.0646 (OUTLIER) cc_final: -0.1022 (mt)
REVERT: A  558 MET cc_start: 0.0582 (OUTLIER) cc_final: -0.0860 (tpp)
REVERT: B   62 ASP cc_start: -0.1369 (m-30) cc_final: -0.1623 (t0)
REVERT: B  121 GLN cc_start: 0.2318 (OUTLIER) cc_final: 0.1909 (mt0)
REVERT: B  136 MET cc_start: 0.3193 (pp-130) cc_final: 0.0889 (mmm)
REVERT: B  209 GLN cc_start: -0.1985 (OUTLIER) cc_final: -0.2309 (mt0)
REVERT: B  211 TYR cc_start: 0.1114 (m-80) cc_final: 0.0501 (t80)
REVERT: B  373 ARG cc_start: -0.1495 (OUTLIER) cc_final: -0.2514 (mmm-85)
REVERT: B  375 LEU cc_start: -0.1739 (OUTLIER) cc_final: -0.2061 (mt)
REVERT: B  413 LYS cc_start: 0.2750 (OUTLIER) cc_final: 0.2249 (mmtt)
REVERT: B  462 MET cc_start: 0.3158 (OUTLIER) cc_final: -0.0046 (pmm)
REVERT: B  487 MET cc_start: 0.3296 (mpp) cc_final: 0.3002 (mtm)
  outliers start: 31
  outliers final: 17
  residues processed: 67
  average time/residue: 1.0898
  time to fit residues: 79.6805
Evaluate side-chains
  66 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 39
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
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  532 LEU
Chi-restraints excluded: chain A residue  539 LEU
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   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  121 GLN
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  279 LEU
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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    8.9990
   chunk 99 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 104 optimal weight:    3.9990
   chunk 71 optimal weight:    0.0670
   chunk 55 optimal weight:    0.0770
   chunk 95 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 74 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   chunk 102 optimal weight:    6.9990
   overall best weight:    0.5276

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

Flipped N/Q/H residues before XYZ refinement:
** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 281 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5124 r_free = 0.5124 target = 0.309001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.246334 restraints weight = 19650.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.4559 rms_B_bonded: 4.92
r_work: 0.4332 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4348 r_free = 0.4348    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4348 r_free = 0.4348    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0320
moved from start:          0.6239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8987  Z= 0.120
  Angle     :  0.749  22.584  12219  Z= 0.308
  Chirality :  0.043   0.183   1325
  Planarity :  0.005   0.060   1590
  Dihedral  :  7.162 142.702   1274
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.79 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 26.15 %
    Favored  : 70.44 %
  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:  0.03 (0.26), residues: 1086
  helix:  1.16 (0.27), residues: 396
  sheet: -0.40 (0.39), residues: 188
  loop : -0.67 (0.28), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 348 
 HIS   0.007   0.001   HIS B 134 
 PHE   0.014   0.001   PHE A 161 
 TYR   0.013   0.001   TYR B 188 
 ARG   0.005   0.000   ARG B 345 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03003 (  355)
  hydrogen bonds       : angle       4.71117 ( 1006)
  metal coordination   : bond        0.00559 (    4)
  metal coordination   : angle      11.51463 (   12)
  covalent geometry    : bond        0.00268 ( 8980)
  covalent geometry    : angle       0.65682 (12207)
  Misc. bond           : bond        0.01218 (    3)

*********************** 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
  72 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 41
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.0671 (OUTLIER) cc_final: -0.1011 (p0)
REVERT: A  532 LEU cc_start: -0.0322 (OUTLIER) cc_final: -0.0725 (mt)
REVERT: A  539 LEU cc_start: -0.0689 (OUTLIER) cc_final: -0.1035 (mt)
REVERT: A  558 MET cc_start: 0.0502 (OUTLIER) cc_final: -0.0852 (tpp)
REVERT: B   62 ASP cc_start: -0.1438 (OUTLIER) cc_final: -0.1820 (t0)
REVERT: B  136 MET cc_start: 0.3096 (pp-130) cc_final: 0.0894 (mmm)
REVERT: B  209 GLN cc_start: -0.1941 (OUTLIER) cc_final: -0.2598 (mt0)
REVERT: B  211 TYR cc_start: 0.0956 (m-80) cc_final: 0.0410 (t80)
REVERT: B  370 TYR cc_start: 0.2269 (m-10) cc_final: 0.2017 (OUTLIER)
REVERT: B  373 ARG cc_start: -0.1417 (OUTLIER) cc_final: -0.2699 (mmm-85)
REVERT: B  413 LYS cc_start: 0.2581 (OUTLIER) cc_final: 0.2108 (mmtt)
REVERT: B  462 MET cc_start: 0.3066 (OUTLIER) cc_final: -0.0138 (pmm)
REVERT: B  487 MET cc_start: 0.3257 (mpp) cc_final: 0.2948 (mtm)
  outliers start: 31
  outliers final: 18
  residues processed: 63
  average time/residue: 1.0251
  time to fit residues: 70.6386
Evaluate side-chains
  65 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 39
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
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  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  532 LEU
Chi-restraints excluded: chain A residue  539 LEU
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   59 GLN
Chi-restraints excluded: chain B residue   62 ASP
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  373 ARG
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0060
   chunk 27 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 89 optimal weight:    5.9990
   chunk 0 optimal weight:    0.9990
   chunk 105 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 85 optimal weight:    5.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5136 r_free = 0.5136 target = 0.310906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.249047 restraints weight = 21723.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.4571 rms_B_bonded: 6.37
r_work: 0.4344 rms_B_bonded: 5.33 restraints_weight: 2.0000
r_work (final): 0.4344
-------------------------------------------------------------------------------
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 = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-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: 0.0317
moved from start:          0.6567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8987  Z= 0.123
  Angle     :  0.763  22.310  12219  Z= 0.318
  Chirality :  0.043   0.175   1325
  Planarity :  0.005   0.065   1590
  Dihedral  :  7.152 142.233   1274
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.34 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 27.03 %
    Favored  : 69.67 %
  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:  1.19 (0.27), residues: 397
  sheet: -0.32 (0.40), residues: 183
  loop : -0.69 (0.27), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 197 
 HIS   0.006   0.001   HIS B 134 
 PHE   0.013   0.001   PHE A 161 
 TYR   0.012   0.001   TYR B 188 
 ARG   0.009   0.000   ARG B  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03058 (  355)
  hydrogen bonds       : angle       4.68129 ( 1006)
  metal coordination   : bond        0.00567 (    4)
  metal coordination   : angle      11.22147 (   12)
  covalent geometry    : bond        0.00275 ( 8980)
  covalent geometry    : angle       0.67779 (12207)
  Misc. bond           : bond        0.01139 (    3)

*********************** 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
  69 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 39
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.0572 (OUTLIER) cc_final: -0.1124 (p0)
REVERT: A  532 LEU cc_start: -0.0255 (OUTLIER) cc_final: -0.0610 (mt)
REVERT: A  539 LEU cc_start: -0.0715 (OUTLIER) cc_final: -0.0975 (mt)
REVERT: A  558 MET cc_start: 0.0344 (OUTLIER) cc_final: -0.0916 (tpp)
REVERT: B   20 ARG cc_start: 0.2522 (tmm160) cc_final: 0.1443 (tmt170)
REVERT: B  136 MET cc_start: 0.3094 (pp-130) cc_final: 0.0878 (mmm)
REVERT: B  209 GLN cc_start: -0.1862 (OUTLIER) cc_final: -0.2531 (mt0)
REVERT: B  211 TYR cc_start: 0.1008 (m-80) cc_final: 0.0336 (t80)
REVERT: B  413 LYS cc_start: 0.2571 (OUTLIER) cc_final: 0.2121 (mmtt)
REVERT: B  462 MET cc_start: 0.3230 (OUTLIER) cc_final: -0.0077 (pmm)
REVERT: B  487 MET cc_start: 0.3294 (mpp) cc_final: 0.2991 (mtm)
  outliers start: 30
  outliers final: 21
  residues processed: 61
  average time/residue: 1.0297
  time to fit residues: 68.7288
Evaluate side-chains
  66 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 38
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
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  532 LEU
Chi-restraints excluded: chain A residue  539 LEU
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   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  233 ASN
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 69 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 16 optimal weight:   20.0000
   chunk 27 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 103 optimal weight:    7.9990
   chunk 1 optimal weight:    0.4980
   chunk 36 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5141 r_free = 0.5141 target = 0.310718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.251725 restraints weight = 28227.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.4621 rms_B_bonded: 7.62
r_work: 0.4326 rms_B_bonded: 5.75 restraints_weight: 2.0000
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4331
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4331 r_free = 0.4331    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4331 r_free = 0.4331    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4331
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0336
moved from start:          0.6705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8987  Z= 0.128
  Angle     :  0.767  22.104  12219  Z= 0.322
  Chirality :  0.043   0.190   1325
  Planarity :  0.005   0.060   1590
  Dihedral  :  7.176 141.965   1274
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.53 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 27.14 %
    Favored  : 69.78 %
  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:  0.04 (0.26), residues: 1086
  helix:  1.14 (0.27), residues: 398
  sheet: -0.31 (0.40), residues: 183
  loop : -0.69 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 542 
 HIS   0.006   0.001   HIS B 134 
 PHE   0.015   0.001   PHE A 161 
 TYR   0.014   0.001   TYR A 527 
 ARG   0.009   0.000   ARG B  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03103 (  355)
  hydrogen bonds       : angle       4.72478 ( 1006)
  metal coordination   : bond        0.00631 (    4)
  metal coordination   : angle      11.10013 (   12)
  covalent geometry    : bond        0.00285 ( 8980)
  covalent geometry    : angle       0.68437 (12207)
  Misc. bond           : bond        0.01306 (    3)

********************** 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
  67 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 39
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 ASN cc_start: 0.0605 (OUTLIER) cc_final: -0.1163 (p0)
REVERT: A  532 LEU cc_start: -0.0103 (OUTLIER) cc_final: -0.0499 (mt)
REVERT: A  539 LEU cc_start: -0.0646 (OUTLIER) cc_final: -0.0878 (mt)
REVERT: A  558 MET cc_start: 0.0331 (OUTLIER) cc_final: -0.0872 (tpp)
REVERT: B   20 ARG cc_start: 0.2513 (tmm160) cc_final: 0.1434 (tmt170)
REVERT: B  121 GLN cc_start: 0.2178 (OUTLIER) cc_final: 0.1716 (mt0)
REVERT: B  136 MET cc_start: 0.3114 (pp-130) cc_final: 0.0878 (mmm)
REVERT: B  209 GLN cc_start: -0.1792 (OUTLIER) cc_final: -0.2293 (mt0)
REVERT: B  211 TYR cc_start: 0.1050 (m-80) cc_final: 0.0303 (t80)
REVERT: B  413 LYS cc_start: 0.2550 (OUTLIER) cc_final: 0.2098 (mmtt)
REVERT: B  462 MET cc_start: 0.3159 (OUTLIER) cc_final: -0.0155 (pmm)
REVERT: B  487 MET cc_start: 0.3302 (mpp) cc_final: 0.2999 (mtm)
  outliers start: 28
  outliers final: 20
  residues processed: 59
  average time/residue: 1.0115
  time to fit residues: 65.6148
Evaluate side-chains
  67 residues out of total 902 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 39
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
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  532 LEU
Chi-restraints excluded: chain A residue  539 LEU
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   59 GLN
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  100 ASP
Chi-restraints excluded: chain B residue  121 GLN
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  186 ARG
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  209 GLN
Chi-restraints excluded: chain B residue  221 VAL
Chi-restraints excluded: chain B residue  233 ASN
Chi-restraints excluded: chain B residue  377 THR
Chi-restraints excluded: chain B residue  413 LYS
Chi-restraints excluded: chain B residue  462 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 58 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0970
   chunk 19 optimal weight:    0.0030
   chunk 72 optimal weight:    0.7980
   chunk 31 optimal weight:   10.0000
   chunk 42 optimal weight:    0.4980
   chunk 103 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0050
   overall best weight:    0.2802

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

Flipped N/Q/H residues before XYZ refinement:
** A 548 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5147 r_free = 0.5147 target = 0.311462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 81)----------------|
| r_work = 0.4630 r_free = 0.4630 target = 0.249319 restraints weight = 22149.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.4575 rms_B_bonded: 5.54
r_work: 0.4356 rms_B_bonded: 5.34 restraints_weight: 2.0000
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4344 r_free = 0.4344    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4344 r_free = 0.4344    target_work(ls_wunit_k1) = 0.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.0305
moved from start:          0.6717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8987  Z= 0.110
  Angle     :  0.732  21.386  12219  Z= 0.299
  Chirality :  0.042   0.177   1325
  Planarity :  0.005   0.061   1590
  Dihedral  :  7.013 142.653   1274
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.60 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 28.13 %
    Favored  : 69.67 %
  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:  0.23 (0.26), residues: 1086
  helix:  1.34 (0.27), residues: 399
  sheet: -0.31 (0.40), residues: 183
  loop : -0.58 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 542 
 HIS   0.008   0.001   HIS B 134 
 PHE   0.012   0.001   PHE A 161 
 TYR   0.012   0.001   TYR B 188 
 ARG   0.008   0.000   ARG B  20 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02825 (  355)
  hydrogen bonds       : angle       4.55713 ( 1006)
  metal coordination   : bond        0.00418 (    4)
  metal coordination   : angle      11.28388 (   12)
  covalent geometry    : bond        0.00246 ( 8980)
  covalent geometry    : angle       0.64088 (12207)
  Misc. bond           : bond        0.00775 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6788.49 seconds
wall clock time: 117 minutes 29.84 seconds (7049.84 seconds total)