Starting phenix.real_space_refine
on Tue Feb  3 20:23:01 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9s4k_54567/02_2026/9s4k_54567.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9s4k_54567/02_2026/9s4k_54567.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9s4k_54567/02_2026/9s4k_54567.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9s4k_54567/02_2026/9s4k_54567.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9s4k_54567/02_2026/9s4k_54567.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9s4k_54567/02_2026/9s4k_54567.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.019
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: 5
    Type Number    sf(0)   Gaussians
     Fe      2      7.16       5
     S      12      5.16       5
     C    4211      2.51       5
     N    1082      2.21       5
     O    1247      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6554
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1062
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 140, 1062
          Classifications: {'peptide': 140}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 132}
    Chain: "B"
      Number of atoms: 1116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 1116
          Classifications: {'peptide': 145}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 137}
    Chain: "C"
      Number of atoms: 2687
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2687
          Classifications: {'peptide': 328}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 312}
    Chain: "D"
      Number of atoms: 1603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1603
          Classifications: {'peptide': 193}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 182}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.40, per 1000 atoms: 0.21
  Number of scatterers: 6554
  At special positions: 0
  Unit cell: (102.208, 97.2462, 117.092, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe      2     26.01
     S      12     16.00
     O    1247      8.00
     N    1082      7.00
     C    4211      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 184.7 milliseconds
  

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1538

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 7 sheets defined
      45.8% alpha, 23.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 16
      removed outlier: 3.804A  pdb=" N   LYS A  16 " --> pdb=" O   ALA A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 19
      No H-bonds generated for 'chain 'A' and resid 17 through 19'
    Processing helix  chain 'A' and resid 20 through 36
      removed outlier: 3.561A  pdb=" N   PHE A  36 " --> pdb=" O   MET A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 43
      removed outlier: 3.700A  pdb=" N   THR A  41 " --> pdb=" O   THR A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 4.038A  pdb=" N   ALA A  79 " --> pdb=" O   ASP A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 90
    Processing helix  chain 'A' and resid 94 through 113
      removed outlier: 4.022A  pdb=" N   PHE A  98 " --> pdb=" O   ASP A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 137
    Processing helix  chain 'B' and resid 4 through 17
      removed outlier: 3.857A  pdb=" N   LYS B  17 " --> pdb=" O   ALA B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 34
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 57 through 77
      removed outlier: 3.603A  pdb=" N   LYS B  61 " --> pdb=" O   ASN B  57 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   HIS B  77 " --> pdb=" O   ASP B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 94
    Processing helix  chain 'B' and resid 101 through 116
      removed outlier: 3.549A  pdb=" N   LEU B 105 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLY B 107 " --> pdb=" O   PHE B 103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 122
      removed outlier: 7.505A  pdb=" N   LYS B 120 " --> pdb=" O   HIS B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 142
    Processing helix  chain 'B' and resid 143 through 146
    Processing helix  chain 'C' and resid 329 through 335
    Processing helix  chain 'C' and resid 336 through 340
      removed outlier: 4.106A  pdb=" N   ILE C 339 " --> pdb=" O   ASN C 336 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 369
    Processing helix  chain 'C' and resid 471 through 487
      Proline residue:  C 483  - end of helix
      removed outlier: 3.529A  pdb=" N   ALA C 487 " --> pdb=" O   PRO C 483 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 489 through 501
      removed outlier: 3.619A  pdb=" N   GLN C 501 " --> pdb=" O   LEU C 497 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 505 through 508
    Processing helix  chain 'C' and resid 509 through 533
      removed outlier: 3.820A  pdb=" N   ASP C 517 " --> pdb=" O   LYS C 513 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 564 through 569
      removed outlier: 4.225A  pdb=" N   PHE C 568 " --> pdb=" O   VAL C 564 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   VAL C 569 " --> pdb=" O   MET C 565 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 564 through 569'
    Processing helix  chain 'D' and resid 332 through 336
    Processing helix  chain 'D' and resid 365 through 370
    Processing helix  chain 'D' and resid 471 through 486
      Proline residue:  D 483  - end of helix
    Processing helix  chain 'D' and resid 489 through 500
      removed outlier: 3.504A  pdb=" N   TYR D 495 " --> pdb=" O   GLU D 491 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 505 through 514
      removed outlier: 4.520A  pdb=" N   ALA D 510 " --> pdb=" O   GLU D 506 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   GLU D 511 " --> pdb=" O   LYS D 507 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TYR D 512 " --> pdb=" O   TYR D 508 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS D 514 " --> pdb=" O   ALA D 510 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 514 through 520
      removed outlier: 4.307A  pdb=" N   GLN D 518 " --> pdb=" O   LYS D 514 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 349 through 352
      removed outlier: 6.319A  pdb=" N   TYR C 421 " --> pdb=" O   TYR C 415 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   TYR C 415 " --> pdb=" O   TYR C 421 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   TYR C 423 " --> pdb=" O   VAL C 413 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 354 through 357
      removed outlier: 5.718A  pdb=" N   HIS C 448 " --> pdb=" O   TYR C 443 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   TYR C 443 " --> pdb=" O   HIS C 448 " (cutoff:3.500A)
      removed outlier: 5.547A  pdb=" N   ASP C 450 " --> pdb=" O   ILE C 441 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   ILE C 441 " --> pdb=" O   ASP C 450 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ASP C 452 " --> pdb=" O   SER C 439 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   SER C 439 " --> pdb=" O   ASP C 452 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG C 433 " --> pdb=" O   PHE C 458 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   GLU C 442 " --> pdb=" O   TRP C 396 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   TRP C 396 " --> pdb=" O   GLU C 442 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 545 through 549
      removed outlier: 4.975A  pdb=" N   ASP C 546 " --> pdb=" O   THR C 577 " (cutoff:3.500A)
      removed outlier: 4.574A  pdb=" N   THR C 577 " --> pdb=" O   ASP C 546 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   TYR C 574 " --> pdb=" O   VAL C 585 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   SER C 615 " --> pdb=" O   LYS C 609 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   LYS C 609 " --> pdb=" O   SER C 615 " (cutoff:3.500A)
      removed outlier: 7.355A  pdb=" N   THR C 617 " --> pdb=" O   VAL C 607 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 552 through 555
      removed outlier: 3.644A  pdb=" N   ASP C 596 " --> pdb=" O   LYS C 634 " (cutoff:3.500A)
      removed outlier: 5.888A  pdb=" N   VAL C 636 " --> pdb=" O   TRP C 594 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   TRP C 594 " --> pdb=" O   VAL C 636 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 552 through 555
      removed outlier: 3.711A  pdb=" N   VAL C 635 " --> pdb=" O   GLY C 644 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TYR C 642 " --> pdb=" O   VAL C 637 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 349 through 352
      removed outlier: 7.752A  pdb=" N   VAL D 372 " --> pdb=" O   LYS D 391 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   LYS D 391 " --> pdb=" O   VAL D 372 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   GLY D 389 " --> pdb=" O   PRO D 374 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER D 414 " --> pdb=" O   TYR D 423 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ARG D 425 " --> pdb=" O   LEU D 412 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   LEU D 412 " --> pdb=" O   ARG D 425 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 354 through 357
      removed outlier: 5.580A  pdb=" N   HIS D 448 " --> pdb=" O   TYR D 443 " (cutoff:3.500A)
      removed outlier: 7.696A  pdb=" N   TYR D 443 " --> pdb=" O   HIS D 448 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   ASP D 450 " --> pdb=" O   ILE D 441 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   ILE D 441 " --> pdb=" O   ASP D 450 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   ASP D 452 " --> pdb=" O   SER D 439 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   SER D 439 " --> pdb=" O   ASP D 452 " (cutoff:3.500A)
      removed outlier: 6.068A  pdb=" N   GLU D 442 " --> pdb=" O   TRP D 396 " (cutoff:3.500A)
      removed outlier: 5.098A  pdb=" N   TRP D 396 " --> pdb=" O   GLU D 442 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LYS D 406 " --> pdb=" O   GLU D 403 " (cutoff:3.500A)

    320 hydrogen bonds defined for protein.
    915 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: 0.71

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.23 -     1.39: 2772
        1.39 -     1.56: 3924
        1.56 -     1.72: 0
        1.72 -     1.89: 21
        1.89 -     2.05: 8
  Bond restraints: 6725
  Sorted by residual:
  bond pdb=" N   HIS B   2 "
       pdb=" CA  HIS B   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.96e+00
  bond pdb=" N   GLU C 328 "
       pdb=" CA  GLU C 328 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.90e+00
  bond pdb=" N   GLU D 328 "
       pdb=" CA  GLU D 328 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.79e+00
  bond pdb=" N   LEU A   2 "
       pdb=" CA  LEU A   2 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.76e+00
  bond pdb=" N   PHE C 399 "
       pdb=" CA  PHE C 399 "
    ideal  model  delta    sigma   weight residual
    1.466  1.454  0.012 1.36e-02 5.41e+03 8.38e-01
  ... (remaining 6720 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 8979
        1.54 -     3.07: 135
        3.07 -     4.61: 37
        4.61 -     6.14: 0
        6.14 -     7.68: 4
  Bond angle restraints: 9155
  Sorted by residual:
  angle pdb=" C   PRO C 624 "
        pdb=" N   ASP C 625 "
        pdb=" CA  ASP C 625 "
      ideal   model   delta    sigma   weight residual
     121.54  129.22   -7.68 1.91e+00 2.74e-01 1.62e+01
  angle pdb=" N   PHE C 534 "
        pdb=" CA  PHE C 534 "
        pdb=" C   PHE C 534 "
      ideal   model   delta    sigma   weight residual
     114.75  110.23    4.52 1.26e+00 6.30e-01 1.29e+01
  angle pdb=" CA  HIS C 551 "
        pdb=" C   HIS C 551 "
        pdb=" N   PHE C 552 "
      ideal   model   delta    sigma   weight residual
     114.87  118.43   -3.56 1.55e+00 4.16e-01 5.28e+00
  angle pdb=" CA  PHE C 534 "
        pdb=" C   PHE C 534 "
        pdb=" N   GLU C 535 "
      ideal   model   delta    sigma   weight residual
     119.80  116.75    3.05 1.34e+00 5.57e-01 5.18e+00
  angle pdb=" CA  PRO C 572 "
        pdb=" C   PRO C 572 "
        pdb=" O   PRO C 572 "
      ideal   model   delta    sigma   weight residual
     123.16  119.92    3.24 1.49e+00 4.50e-01 4.72e+00
  ... (remaining 9150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 3736
       17.99 -    35.98: 212
       35.98 -    53.96: 35
       53.96 -    71.95: 7
       71.95 -    89.94: 6
  Dihedral angle restraints: 3996
    sinusoidal: 1613
      harmonic: 2383
  Sorted by residual:
  dihedral pdb=" CA  GLU C 533 "
           pdb=" C   GLU C 533 "
           pdb=" N   PHE C 534 "
           pdb=" CA  PHE C 534 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.16   21.84     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" C2B HEM A 201 "
           pdb=" C3B HEM A 201 "
           pdb=" CAB HEM A 201 "
           pdb=" CBB HEM A 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
      -0.00  -35.25   35.25     2      1.00e+01 1.00e-02 1.60e+01
  dihedral pdb=" C2D HEM B 201 "
           pdb=" C3D HEM B 201 "
           pdb=" CAD HEM B 201 "
           pdb=" CBD HEM B 201 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.94  -89.94     2      2.00e+01 2.50e-03 1.20e+01
  ... (remaining 3993 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 631
       0.030 -    0.060: 253
       0.060 -    0.089: 47
       0.089 -    0.119: 54
       0.119 -    0.149: 8
  Chirality restraints: 993
  Sorted by residual:
  chirality pdb=" CA  VAL C 553 "
            pdb=" N   VAL C 553 "
            pdb=" C   VAL C 553 "
            pdb=" CB  VAL C 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.55e-01
  chirality pdb=" CA  VAL C 584 "
            pdb=" N   VAL C 584 "
            pdb=" C   VAL C 584 "
            pdb=" CB  VAL C 584 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.65e-01
  chirality pdb=" CA  ILE C 447 "
            pdb=" N   ILE C 447 "
            pdb=" C   ILE C 447 "
            pdb=" CB  ILE C 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.60e-01
  ... (remaining 990 not shown)

  Planarity restraints: 1169
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  37 "    0.010 2.00e-02 2.50e+03   1.02e-02 2.62e+00
        pdb=" CG  TRP B  37 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  37 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  37 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  37 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  37 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  37 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  37 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  37 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  37 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B   4 "   -0.024 5.00e-02 4.00e+02   3.62e-02 2.10e+00
        pdb=" N   PRO B   5 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO B   5 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B   5 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B  99 "   -0.024 5.00e-02 4.00e+02   3.59e-02 2.06e+00
        pdb=" N   PRO B 100 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 100 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 100 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 1166 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1307
        2.78 -     3.31: 6724
        3.31 -     3.84: 10515
        3.84 -     4.37: 12296
        4.37 -     4.90: 20756
  Nonbonded interactions: 51598
  Sorted by model distance:
  nonbonded pdb=" O   PRO C 624 "
            pdb=" OD1 ASP C 625 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   GLU C 522 "
            pdb=" OD1 ASP C 525 "
     model   vdw
     2.343 3.040
  nonbonded pdb=" OD1 ASP C 347 "
            pdb=" OD1 ASN C 348 "
     model   vdw
     2.389 3.040
  nonbonded pdb=" O   LEU B  31 "
            pdb=" O   VAL B  34 "
     model   vdw
     2.439 3.040
  nonbonded pdb=" O   LYS D 391 "
            pdb=" OG1 THR D 392 "
     model   vdw
     2.446 3.040
  ... (remaining 51593 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.040
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
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      :  0.003   0.054   6727  Z= 0.115
  Angle     :  0.539   7.676   9155  Z= 0.288
  Chirality :  0.040   0.149    993
  Planarity :  0.004   0.037   1169
  Dihedral  : 12.100  89.938   2458
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  4.69 %
    Favored  : 94.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.31), residues: 798
  helix:  0.97 (0.31), residues: 315
  sheet: -1.46 (0.38), residues: 169
  loop : -0.55 (0.38), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 616 
 TYR   0.011   0.001   TYR C 475 
 PHE   0.007   0.001   PHE C 365 
 TRP   0.028   0.001   TRP B  37 
 HIS   0.002   0.001   HIS B 116 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 6725)
  covalent geometry    : angle       0.53863 ( 9155)
  hydrogen bonds       : bond        0.16526 (  312)
  hydrogen bonds       : angle       6.86364 (  915)
  Misc. bond           : bond        0.03733 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 226
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 ASP cc_start: 0.8202 (t0) cc_final: 0.7383 (t0)
REVERT: B    6 GLU cc_start: 0.8552 (mm-30) cc_final: 0.7665 (mm-30)
REVERT: B    7 GLU cc_start: 0.8560 (tp30) cc_final: 0.8099 (tp30)
REVERT: B  102 ASN cc_start: 0.9257 (m-40) cc_final: 0.8702 (m-40)
REVERT: B  108 ASN cc_start: 0.9443 (m-40) cc_final: 0.9151 (m-40)
REVERT: B  127 GLN cc_start: 0.8785 (tm-30) cc_final: 0.8396 (tm-30)
REVERT: C  388 LEU cc_start: 0.8753 (tp) cc_final: 0.8225 (tp)
REVERT: D  390 LEU cc_start: 0.9179 (mp) cc_final: 0.8959 (mp)
REVERT: D  426 PHE cc_start: 0.8223 (p90) cc_final: 0.7840 (p90)
REVERT: D  477 LEU cc_start: 0.9092 (tp) cc_final: 0.8892 (tp)
  outliers start: 4
  outliers final: 1
  residues processed: 227
  average time/residue: 0.1083
  time to fit residues: 30.1935
Evaluate side-chains
  113 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  419 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.0980
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    2.4186

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

Flipped N/Q/H residues before XYZ refinement:
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 146 HIS
D 464 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.041355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.030550 restraints weight = 48737.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.031631 restraints weight = 33008.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.032472 restraints weight = 24905.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.033101 restraints weight = 19999.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.033564 restraints weight = 16818.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.095   6727  Z= 0.206
  Angle     :  0.721   8.821   9155  Z= 0.372
  Chirality :  0.047   0.201    993
  Planarity :  0.005   0.038   1169
  Dihedral  :  7.976  77.484    888
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 13.49 %
    Favored  : 84.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.30), residues: 798
  helix:  0.65 (0.29), residues: 318
  sheet: -1.11 (0.40), residues: 157
  loop : -0.62 (0.37), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 520 
 TYR   0.016   0.002   TYR A  24 
 PHE   0.025   0.003   PHE B  85 
 TRP   0.027   0.003   TRP C 594 
 HIS   0.005   0.001   HIS C 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00519 ( 6725)
  covalent geometry    : angle       0.72135 ( 9155)
  hydrogen bonds       : bond        0.03762 (  312)
  hydrogen bonds       : angle       5.28763 (  915)
  Misc. bond           : bond        0.07712 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9323 (m-40) cc_final: 0.9101 (m110)
REVERT: A   27 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8742 (mt-10)
REVERT: A   74 ASP cc_start: 0.8350 (p0) cc_final: 0.8022 (p0)
REVERT: B    7 GLU cc_start: 0.9438 (tp30) cc_final: 0.8877 (tp30)
REVERT: B   59 LYS cc_start: 0.9496 (mmtt) cc_final: 0.9290 (mmtm)
REVERT: B  102 ASN cc_start: 0.9640 (m-40) cc_final: 0.9373 (m110)
REVERT: B  108 ASN cc_start: 0.9737 (m-40) cc_final: 0.9502 (m-40)
REVERT: B  127 GLN cc_start: 0.9478 (tm-30) cc_final: 0.9003 (tm-30)
REVERT: B  145 TYR cc_start: 0.8342 (m-80) cc_final: 0.8039 (m-80)
REVERT: C  460 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8787 (pt0)
REVERT: C  603 ARG cc_start: 0.9186 (ptp-110) cc_final: 0.8472 (ttm170)
REVERT: D  336 ASN cc_start: 0.9256 (p0) cc_final: 0.8933 (p0)
REVERT: D  365 PHE cc_start: 0.8612 (t80) cc_final: 0.8392 (t80)
REVERT: D  388 LEU cc_start: 0.9557 (mp) cc_final: 0.9228 (mp)
REVERT: D  426 PHE cc_start: 0.9345 (p90) cc_final: 0.9137 (p90)
  outliers start: 16
  outliers final: 8
  residues processed: 123
  average time/residue: 0.0737
  time to fit residues: 11.8172
Evaluate side-chains
  105 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain C residue  460 GLN
Chi-restraints excluded: chain C residue  471 ASP
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  565 MET
Chi-restraints excluded: chain C residue  575 THR
Chi-restraints excluded: chain C residue  637 VAL
Chi-restraints excluded: chain D residue  462 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 29 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 73 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 32 optimal weight:    0.3980
   chunk 58 optimal weight:    8.9990
   chunk 78 optimal weight:    0.6980
   chunk 36 optimal weight:   20.0000
   chunk 35 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 464 ASN
D 464 ASN
D 476 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.040597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.029940 restraints weight = 46560.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.031026 restraints weight = 30997.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.031849 restraints weight = 23080.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.032488 restraints weight = 18397.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.032968 restraints weight = 15398.393|
|-----------------------------------------------------------------------------|
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.4464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.091   6727  Z= 0.175
  Angle     :  0.679  12.068   9155  Z= 0.343
  Chirality :  0.045   0.156    993
  Planarity :  0.004   0.042   1169
  Dihedral  :  7.487  77.064    884
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.62 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.30), residues: 798
  helix:  0.75 (0.29), residues: 319
  sheet: -1.18 (0.38), residues: 168
  loop : -0.63 (0.37), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 104 
 TYR   0.021   0.002   TYR B  35 
 PHE   0.020   0.002   PHE B  85 
 TRP   0.015   0.002   TRP B  37 
 HIS   0.004   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6725)
  covalent geometry    : angle       0.67913 ( 9155)
  hydrogen bonds       : bond        0.03498 (  312)
  hydrogen bonds       : angle       5.01598 (  915)
  Misc. bond           : bond        0.06656 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 ASN cc_start: 0.9319 (m-40) cc_final: 0.9109 (m110)
REVERT: A   27 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8401 (pt0)
REVERT: A   85 ASP cc_start: 0.9537 (t0) cc_final: 0.9331 (t0)
REVERT: B    6 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8287 (mm-30)
REVERT: B    7 GLU cc_start: 0.9442 (tp30) cc_final: 0.8877 (tp30)
REVERT: B  102 ASN cc_start: 0.9655 (m-40) cc_final: 0.9382 (m110)
REVERT: B  108 ASN cc_start: 0.9700 (m-40) cc_final: 0.9379 (m-40)
REVERT: B  145 TYR cc_start: 0.8355 (m-80) cc_final: 0.7724 (m-10)
REVERT: C  356 MET cc_start: 0.9531 (mmm) cc_final: 0.9303 (mmm)
REVERT: C  458 PHE cc_start: 0.9475 (m-80) cc_final: 0.9144 (m-80)
REVERT: C  460 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8841 (pt0)
REVERT: C  603 ARG cc_start: 0.9178 (ptp-110) cc_final: 0.8513 (ttm170)
REVERT: D  336 ASN cc_start: 0.9299 (p0) cc_final: 0.8948 (p0)
REVERT: D  388 LEU cc_start: 0.9547 (mp) cc_final: 0.9216 (mp)
REVERT: D  426 PHE cc_start: 0.9361 (p90) cc_final: 0.9157 (p90)
  outliers start: 15
  outliers final: 9
  residues processed: 113
  average time/residue: 0.0681
  time to fit residues: 10.1478
Evaluate side-chains
  100 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain C residue  381 LYS
Chi-restraints excluded: chain C residue  460 GLN
Chi-restraints excluded: chain C residue  471 ASP
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  565 MET
Chi-restraints excluded: chain C residue  575 THR
Chi-restraints excluded: chain D residue  378 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 78 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 55 optimal weight:    8.9990
   chunk 74 optimal weight:    0.7980
   chunk 30 optimal weight:    8.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
D 464 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.040799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.030028 restraints weight = 46716.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.031155 restraints weight = 30953.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.032003 restraints weight = 23015.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2737 r_free = 0.2737 target = 0.032677 restraints weight = 18296.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.033158 restraints weight = 15244.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8676
moved from start:          0.4917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6727  Z= 0.135
  Angle     :  0.641  10.358   9155  Z= 0.320
  Chirality :  0.044   0.145    993
  Planarity :  0.004   0.040   1169
  Dihedral  :  7.268  78.315    884
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.19 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.27 (0.30), residues: 798
  helix:  0.93 (0.30), residues: 319
  sheet: -1.11 (0.38), residues: 170
  loop : -0.66 (0.37), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 104 
 TYR   0.013   0.001   TYR B  35 
 PHE   0.018   0.002   PHE C 426 
 TRP   0.012   0.001   TRP A  14 
 HIS   0.006   0.001   HIS A  89 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6725)
  covalent geometry    : angle       0.64115 ( 9155)
  hydrogen bonds       : bond        0.03179 (  312)
  hydrogen bonds       : angle       4.82210 (  915)
  Misc. bond           : bond        0.04956 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8358 (pt0)
REVERT: B    7 GLU cc_start: 0.9487 (tp30) cc_final: 0.8985 (tp30)
REVERT: B  102 ASN cc_start: 0.9658 (m-40) cc_final: 0.9391 (m110)
REVERT: B  108 ASN cc_start: 0.9647 (m-40) cc_final: 0.9413 (m-40)
REVERT: B  145 TYR cc_start: 0.8417 (m-80) cc_final: 0.7723 (m-10)
REVERT: C  356 MET cc_start: 0.9577 (mmm) cc_final: 0.9362 (mmm)
REVERT: C  458 PHE cc_start: 0.9524 (m-80) cc_final: 0.9084 (m-80)
REVERT: C  460 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8753 (pt0)
REVERT: C  603 ARG cc_start: 0.9154 (ptp-110) cc_final: 0.8548 (ttm170)
REVERT: C  619 ILE cc_start: 0.9340 (OUTLIER) cc_final: 0.9126 (tt)
REVERT: D  336 ASN cc_start: 0.9321 (p0) cc_final: 0.8990 (p0)
REVERT: D  388 LEU cc_start: 0.9519 (mp) cc_final: 0.9208 (mp)
REVERT: D  426 PHE cc_start: 0.9338 (p90) cc_final: 0.9041 (p90)
  outliers start: 19
  outliers final: 12
  residues processed: 115
  average time/residue: 0.0971
  time to fit residues: 14.3980
Evaluate side-chains
  93 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 79
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  381 LYS
Chi-restraints excluded: chain C residue  460 GLN
Chi-restraints excluded: chain C residue  471 ASP
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  565 MET
Chi-restraints excluded: chain C residue  575 THR
Chi-restraints excluded: chain C residue  619 ILE
Chi-restraints excluded: chain C residue  637 VAL
Chi-restraints excluded: chain D residue  416 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 34 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 53 optimal weight:    8.9990
   chunk 8 optimal weight:   30.0000
   chunk 54 optimal weight:    1.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** B  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  63 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.038527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2586 r_free = 0.2586 target = 0.028002 restraints weight = 49202.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.029062 restraints weight = 32833.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.029844 restraints weight = 24429.038|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.030436 restraints weight = 19495.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.030902 restraints weight = 16354.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.5459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.098   6727  Z= 0.224
  Angle     :  0.685   9.941   9155  Z= 0.348
  Chirality :  0.044   0.169    993
  Planarity :  0.005   0.039   1169
  Dihedral  :  7.168  73.789    884
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.40 %
    Allowed  : 16.05 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.40 (0.30), residues: 798
  helix:  0.88 (0.30), residues: 319
  sheet: -1.17 (0.39), residues: 166
  loop : -0.82 (0.35), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 104 
 TYR   0.014   0.002   TYR C 366 
 PHE   0.017   0.002   PHE D 365 
 TRP   0.011   0.002   TRP C 594 
 HIS   0.008   0.001   HIS C 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 6725)
  covalent geometry    : angle       0.68475 ( 9155)
  hydrogen bonds       : bond        0.03398 (  312)
  hydrogen bonds       : angle       4.91435 (  915)
  Misc. bond           : bond        0.05920 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 75
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8339 (pt0)
REVERT: A   32 MET cc_start: 0.9486 (tpp) cc_final: 0.8868 (tmm)
REVERT: A   60 LYS cc_start: 0.9532 (ptmt) cc_final: 0.9207 (pttp)
REVERT: B    7 GLU cc_start: 0.9463 (tp30) cc_final: 0.9006 (tp30)
REVERT: B  102 ASN cc_start: 0.9647 (m-40) cc_final: 0.9388 (m110)
REVERT: B  108 ASN cc_start: 0.9703 (m-40) cc_final: 0.9466 (m-40)
REVERT: B  145 TYR cc_start: 0.8385 (m-80) cc_final: 0.7704 (m-80)
REVERT: C  458 PHE cc_start: 0.9584 (m-80) cc_final: 0.9141 (m-80)
REVERT: C  460 GLN cc_start: 0.9030 (OUTLIER) cc_final: 0.8762 (pt0)
REVERT: C  619 ILE cc_start: 0.9320 (OUTLIER) cc_final: 0.9091 (tt)
REVERT: D  336 ASN cc_start: 0.9414 (p0) cc_final: 0.9065 (p0)
REVERT: D  388 LEU cc_start: 0.9561 (mp) cc_final: 0.9241 (mp)
REVERT: D  426 PHE cc_start: 0.9416 (p90) cc_final: 0.9070 (p90)
  outliers start: 38
  outliers final: 23
  residues processed: 104
  average time/residue: 0.0798
  time to fit residues: 11.1801
Evaluate side-chains
  96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue   54 GLN
Chi-restraints excluded: chain A residue  140 TYR
Chi-restraints excluded: chain B residue   85 PHE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  381 LYS
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  460 GLN
Chi-restraints excluded: chain C residue  471 ASP
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  565 MET
Chi-restraints excluded: chain C residue  575 THR
Chi-restraints excluded: chain C residue  586 MET
Chi-restraints excluded: chain C residue  619 ILE
Chi-restraints excluded: chain C residue  651 ILE
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  378 ILE
Chi-restraints excluded: chain D residue  462 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 36 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   overall best weight:    0.9180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.039863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.029248 restraints weight = 47227.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.030362 restraints weight = 31138.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.031183 restraints weight = 23033.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.031813 restraints weight = 18282.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 16)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.032222 restraints weight = 15279.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8699
moved from start:          0.5554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6727  Z= 0.124
  Angle     :  0.655  11.472   9155  Z= 0.322
  Chirality :  0.043   0.189    993
  Planarity :  0.004   0.047   1169
  Dihedral  :  7.049  77.531    884
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.47 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.30), residues: 798
  helix:  1.00 (0.30), residues: 328
  sheet: -0.94 (0.39), residues: 169
  loop : -0.86 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 104 
 TYR   0.015   0.001   TYR B  35 
 PHE   0.016   0.002   PHE B  85 
 TRP   0.013   0.001   TRP A  14 
 HIS   0.003   0.001   HIS C 551 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6725)
  covalent geometry    : angle       0.65490 ( 9155)
  hydrogen bonds       : bond        0.03068 (  312)
  hydrogen bonds       : angle       4.69188 (  915)
  Misc. bond           : bond        0.03802 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8351 (pt0)
REVERT: A   60 LYS cc_start: 0.9545 (ptmt) cc_final: 0.9248 (pttp)
REVERT: B    7 GLU cc_start: 0.9493 (tp30) cc_final: 0.9024 (tp30)
REVERT: B  102 ASN cc_start: 0.9664 (m-40) cc_final: 0.9433 (m110)
REVERT: B  108 ASN cc_start: 0.9634 (m-40) cc_final: 0.9392 (m-40)
REVERT: B  120 LYS cc_start: 0.9751 (OUTLIER) cc_final: 0.9488 (ptpp)
REVERT: B  145 TYR cc_start: 0.8426 (m-80) cc_final: 0.7714 (m-80)
REVERT: C  356 MET cc_start: 0.9584 (mmm) cc_final: 0.9196 (mmm)
REVERT: C  456 MET cc_start: 0.9634 (ttt) cc_final: 0.8722 (tmm)
REVERT: C  458 PHE cc_start: 0.9543 (m-80) cc_final: 0.8953 (m-80)
REVERT: C  460 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8730 (pt0)
REVERT: C  603 ARG cc_start: 0.9146 (ptp-110) cc_final: 0.8525 (ttm170)
REVERT: C  619 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9081 (tt)
REVERT: D  336 ASN cc_start: 0.9418 (p0) cc_final: 0.9129 (p0)
REVERT: D  388 LEU cc_start: 0.9522 (mp) cc_final: 0.9191 (mp)
REVERT: D  426 PHE cc_start: 0.9437 (p90) cc_final: 0.9034 (p90)
  outliers start: 21
  outliers final: 16
  residues processed: 103
  average time/residue: 0.0851
  time to fit residues: 11.4149
Evaluate side-chains
  95 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   41 PHE
Chi-restraints excluded: chain B residue   71 PHE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue  381 LYS
Chi-restraints excluded: chain C residue  460 GLN
Chi-restraints excluded: chain C residue  471 ASP
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  565 MET
Chi-restraints excluded: chain C residue  575 THR
Chi-restraints excluded: chain C residue  586 MET
Chi-restraints excluded: chain C residue  619 ILE
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  378 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0670
   chunk 30 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.7922

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

Flipped N/Q/H residues before XYZ refinement:
C 331 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.040373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.029776 restraints weight = 46241.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2690 r_free = 0.2690 target = 0.030892 restraints weight = 30632.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.031735 restraints weight = 22712.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.032351 restraints weight = 18052.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.032834 restraints weight = 15123.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8689
moved from start:          0.5722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6727  Z= 0.122
  Angle     :  0.671  11.472   9155  Z= 0.327
  Chirality :  0.043   0.173    993
  Planarity :  0.004   0.047   1169
  Dihedral  :  6.934  79.468    884
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 20.74 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.31), residues: 798
  helix:  1.11 (0.30), residues: 328
  sheet: -0.79 (0.39), residues: 169
  loop : -0.81 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 104 
 TYR   0.011   0.001   TYR A 140 
 PHE   0.016   0.001   PHE B  85 
 TRP   0.012   0.001   TRP B  37 
 HIS   0.003   0.000   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6725)
  covalent geometry    : angle       0.67140 ( 9155)
  hydrogen bonds       : bond        0.02999 (  312)
  hydrogen bonds       : angle       4.58243 (  915)
  Misc. bond           : bond        0.01605 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8518 (m-80) cc_final: 0.8058 (m-80)
REVERT: A   27 GLU cc_start: 0.8935 (mt-10) cc_final: 0.8388 (pt0)
REVERT: A   60 LYS cc_start: 0.9559 (ptmt) cc_final: 0.9248 (pttp)
REVERT: B    7 GLU cc_start: 0.9485 (tp30) cc_final: 0.9009 (tp30)
REVERT: B  102 ASN cc_start: 0.9684 (m-40) cc_final: 0.9422 (m110)
REVERT: B  108 ASN cc_start: 0.9632 (m-40) cc_final: 0.9381 (m-40)
REVERT: B  120 LYS cc_start: 0.9735 (OUTLIER) cc_final: 0.9466 (ptpp)
REVERT: B  145 TYR cc_start: 0.8441 (m-80) cc_final: 0.7681 (m-80)
REVERT: C  356 MET cc_start: 0.9589 (mmm) cc_final: 0.9265 (mmm)
REVERT: C  456 MET cc_start: 0.9625 (ttt) cc_final: 0.8677 (tmm)
REVERT: C  458 PHE cc_start: 0.9530 (m-80) cc_final: 0.8878 (m-80)
REVERT: C  460 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8655 (pt0)
REVERT: C  603 ARG cc_start: 0.9134 (ptp-110) cc_final: 0.8558 (mtm180)
REVERT: C  619 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9022 (tt)
REVERT: D  388 LEU cc_start: 0.9501 (mp) cc_final: 0.9185 (mp)
REVERT: D  426 PHE cc_start: 0.9440 (p90) cc_final: 0.9019 (p90)
  outliers start: 24
  outliers final: 17
  residues processed: 108
  average time/residue: 0.0799
  time to fit residues: 11.7439
Evaluate side-chains
  97 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain B residue   71 PHE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  381 LYS
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  460 GLN
Chi-restraints excluded: chain C residue  471 ASP
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  565 MET
Chi-restraints excluded: chain C residue  575 THR
Chi-restraints excluded: chain C residue  586 MET
Chi-restraints excluded: chain C residue  619 ILE
Chi-restraints excluded: chain D residue  377 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A   9 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.038899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.028381 restraints weight = 50279.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.029458 restraints weight = 33469.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.030241 restraints weight = 24954.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.030831 restraints weight = 19988.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.031277 restraints weight = 16845.917|
|-----------------------------------------------------------------------------|
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8757
moved from start:          0.5961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086   6727  Z= 0.192
  Angle     :  0.702  14.248   9155  Z= 0.348
  Chirality :  0.045   0.276    993
  Planarity :  0.005   0.045   1169
  Dihedral  :  6.920  77.928    884
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 15.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 21.59 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.30), residues: 798
  helix:  1.02 (0.30), residues: 329
  sheet: -0.95 (0.39), residues: 167
  loop : -0.81 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 104 
 TYR   0.018   0.002   TYR B  35 
 PHE   0.018   0.002   PHE D 365 
 TRP   0.008   0.001   TRP B  37 
 HIS   0.004   0.001   HIS C 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 6725)
  covalent geometry    : angle       0.70205 ( 9155)
  hydrogen bonds       : bond        0.03317 (  312)
  hydrogen bonds       : angle       4.82044 (  915)
  Misc. bond           : bond        0.04251 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 77
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8349 (pt0)
REVERT: B    7 GLU cc_start: 0.9460 (tp30) cc_final: 0.9003 (tp30)
REVERT: B  102 ASN cc_start: 0.9654 (m-40) cc_final: 0.9398 (m110)
REVERT: B  108 ASN cc_start: 0.9663 (m-40) cc_final: 0.9404 (m-40)
REVERT: B  120 LYS cc_start: 0.9751 (OUTLIER) cc_final: 0.9462 (ptpp)
REVERT: B  145 TYR cc_start: 0.8394 (m-80) cc_final: 0.7610 (m-80)
REVERT: C  356 MET cc_start: 0.9559 (mmm) cc_final: 0.9322 (mmm)
REVERT: C  456 MET cc_start: 0.9639 (ttt) cc_final: 0.8600 (tmm)
REVERT: C  460 GLN cc_start: 0.9015 (OUTLIER) cc_final: 0.8717 (pt0)
REVERT: D  388 LEU cc_start: 0.9548 (mp) cc_final: 0.9300 (mp)
  outliers start: 31
  outliers final: 23
  residues processed: 99
  average time/residue: 0.0782
  time to fit residues: 10.5163
Evaluate side-chains
  96 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   71 PHE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain B residue  121 GLU
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  381 LYS
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  460 GLN
Chi-restraints excluded: chain C residue  471 ASP
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  565 MET
Chi-restraints excluded: chain C residue  575 THR
Chi-restraints excluded: chain C residue  586 MET
Chi-restraints excluded: chain C residue  637 VAL
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  377 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 39 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 50 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** D 336 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 = 0.2985 r_free = 0.2985 target = 0.039617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.029148 restraints weight = 50063.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.030239 restraints weight = 33076.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.031034 restraints weight = 24549.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.031648 restraints weight = 19582.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.032096 restraints weight = 16410.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.6073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   6727  Z= 0.148
  Angle     :  0.702  14.765   9155  Z= 0.345
  Chirality :  0.045   0.218    993
  Planarity :  0.005   0.046   1169
  Dihedral  :  6.922  80.880    884
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 22.02 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.30), residues: 798
  helix:  0.97 (0.30), residues: 329
  sheet: -0.69 (0.40), residues: 165
  loop : -0.81 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 104 
 TYR   0.012   0.001   TYR A 140 
 PHE   0.019   0.002   PHE D 365 
 TRP   0.013   0.001   TRP B  37 
 HIS   0.003   0.001   HIS C 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 6725)
  covalent geometry    : angle       0.70209 ( 9155)
  hydrogen bonds       : bond        0.03159 (  312)
  hydrogen bonds       : angle       4.90163 (  915)
  Misc. bond           : bond        0.03374 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 74
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8603 (m-80) cc_final: 0.8076 (m-80)
REVERT: A   27 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8651 (mt-10)
REVERT: B    7 GLU cc_start: 0.9467 (tp30) cc_final: 0.9007 (tp30)
REVERT: B  102 ASN cc_start: 0.9667 (m-40) cc_final: 0.9421 (m110)
REVERT: B  108 ASN cc_start: 0.9667 (m-40) cc_final: 0.9285 (m-40)
REVERT: B  120 LYS cc_start: 0.9734 (OUTLIER) cc_final: 0.9466 (ptpp)
REVERT: B  145 TYR cc_start: 0.8361 (m-80) cc_final: 0.7550 (m-80)
REVERT: C  356 MET cc_start: 0.9570 (mmm) cc_final: 0.9305 (mmm)
REVERT: C  456 MET cc_start: 0.9625 (ttt) cc_final: 0.8611 (tmm)
REVERT: C  460 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8666 (pt0)
REVERT: C  645 GLN cc_start: 0.8707 (OUTLIER) cc_final: 0.7945 (pp30)
REVERT: D  388 LEU cc_start: 0.9495 (mp) cc_final: 0.9293 (mp)
REVERT: D  456 MET cc_start: 0.9326 (tpp) cc_final: 0.8971 (tpp)
  outliers start: 29
  outliers final: 24
  residues processed: 96
  average time/residue: 0.0802
  time to fit residues: 10.5551
Evaluate side-chains
  100 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 73
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   28 LEU
Chi-restraints excluded: chain B residue   71 PHE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  112 CYS
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  381 LYS
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  460 GLN
Chi-restraints excluded: chain C residue  471 ASP
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  565 MET
Chi-restraints excluded: chain C residue  575 THR
Chi-restraints excluded: chain C residue  586 MET
Chi-restraints excluded: chain C residue  637 VAL
Chi-restraints excluded: chain C residue  645 GLN
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  377 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0870
   chunk 77 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 58 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
** C 551 HIS ** 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 = 0.3010 r_free = 0.3010 target = 0.040627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.030073 restraints weight = 48400.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.031214 restraints weight = 31518.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.032054 restraints weight = 23170.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.032680 restraints weight = 18347.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.033151 restraints weight = 15318.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.6176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6727  Z= 0.125
  Angle     :  0.711  14.963   9155  Z= 0.344
  Chirality :  0.044   0.164    993
  Planarity :  0.004   0.048   1169
  Dihedral  :  6.919  83.594    884
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.73 %
    Favored  : 73.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.31), residues: 798
  helix:  0.98 (0.30), residues: 329
  sheet: -0.64 (0.40), residues: 171
  loop : -0.76 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 104 
 TYR   0.023   0.001   TYR B  35 
 PHE   0.016   0.002   PHE D 365 
 TRP   0.012   0.001   TRP B  37 
 HIS   0.002   0.000   HIS C 647 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6725)
  covalent geometry    : angle       0.71119 ( 9155)
  hydrogen bonds       : bond        0.03067 (  312)
  hydrogen bonds       : angle       4.77721 (  915)
  Misc. bond           : bond        0.02029 (    2)

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

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

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1596 Ramachandran restraints generated.
    798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 TYR cc_start: 0.8588 (m-80) cc_final: 0.8073 (m-80)
REVERT: A   27 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8646 (mt-10)
REVERT: B    7 GLU cc_start: 0.9469 (tp30) cc_final: 0.9033 (tp30)
REVERT: B  102 ASN cc_start: 0.9665 (m-40) cc_final: 0.9424 (m110)
REVERT: B  108 ASN cc_start: 0.9644 (m-40) cc_final: 0.9268 (m-40)
REVERT: B  120 LYS cc_start: 0.9724 (OUTLIER) cc_final: 0.9442 (ptpp)
REVERT: B  121 GLU cc_start: 0.9434 (tt0) cc_final: 0.9159 (tm-30)
REVERT: B  145 TYR cc_start: 0.8398 (m-80) cc_final: 0.7576 (m-80)
REVERT: C  356 MET cc_start: 0.9566 (mmm) cc_final: 0.9252 (mmm)
REVERT: C  456 MET cc_start: 0.9597 (ttt) cc_final: 0.8574 (tmm)
REVERT: C  460 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8651 (pt0)
REVERT: C  594 TRP cc_start: 0.9368 (m100) cc_final: 0.9108 (m100)
REVERT: C  603 ARG cc_start: 0.9154 (ptp-110) cc_final: 0.8594 (mtt180)
REVERT: C  645 GLN cc_start: 0.8644 (OUTLIER) cc_final: 0.7662 (pp30)
REVERT: D  456 MET cc_start: 0.9357 (tpp) cc_final: 0.9011 (tpp)
  outliers start: 25
  outliers final: 19
  residues processed: 101
  average time/residue: 0.0864
  time to fit residues: 11.6390
Evaluate side-chains
  98 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 HIS
Chi-restraints excluded: chain B residue   11 VAL
Chi-restraints excluded: chain B residue   41 PHE
Chi-restraints excluded: chain B residue   71 PHE
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue   99 ASP
Chi-restraints excluded: chain B residue  120 LYS
Chi-restraints excluded: chain C residue  352 ILE
Chi-restraints excluded: chain C residue  377 VAL
Chi-restraints excluded: chain C residue  381 LYS
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  460 GLN
Chi-restraints excluded: chain C residue  471 ASP
Chi-restraints excluded: chain C residue  536 ASN
Chi-restraints excluded: chain C residue  538 THR
Chi-restraints excluded: chain C residue  554 VAL
Chi-restraints excluded: chain C residue  565 MET
Chi-restraints excluded: chain C residue  575 THR
Chi-restraints excluded: chain C residue  637 VAL
Chi-restraints excluded: chain C residue  645 GLN
Chi-restraints excluded: chain D residue  330 LEU
Chi-restraints excluded: chain D residue  377 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0870
   chunk 18 optimal weight:    7.9990
   chunk 62 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 63 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
** C 551 HIS ** 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 = 0.3027 r_free = 0.3027 target = 0.041172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.030724 restraints weight = 47321.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.031845 restraints weight = 31243.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.032673 restraints weight = 23081.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.033309 restraints weight = 18314.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.033787 restraints weight = 15253.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.6278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6727  Z= 0.123
  Angle     :  0.722  15.049   9155  Z= 0.346
  Chirality :  0.044   0.169    993
  Planarity :  0.005   0.046   1169
  Dihedral  :  6.770  83.380    884
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 23.30 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.31), residues: 798
  helix:  1.00 (0.30), residues: 328
  sheet: -0.50 (0.41), residues: 167
  loop : -0.67 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 104 
 TYR   0.012   0.001   TYR A 140 
 PHE   0.019   0.002   PHE A 128 
 TRP   0.013   0.001   TRP B  37 
 HIS   0.003   0.000   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6725)
  covalent geometry    : angle       0.72224 ( 9155)
  hydrogen bonds       : bond        0.03016 (  312)
  hydrogen bonds       : angle       4.74682 (  915)
  Misc. bond           : bond        0.01904 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1160.40 seconds
wall clock time: 20 minutes 49.74 seconds (1249.74 seconds total)