Starting phenix.real_space_refine
on Wed Mar 12 21:26:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bpb_16148/03_2025/8bpb_16148_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bpb_16148/03_2025/8bpb_16148.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bpb_16148/03_2025/8bpb_16148.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bpb_16148/03_2025/8bpb_16148.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bpb_16148/03_2025/8bpb_16148_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bpb_16148/03_2025/8bpb_16148_neut.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      3      6.06       5
     S      55      5.16       5
     C    5329      2.51       5
     N    1447      2.21       5
     O    1548      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8384
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4403
          Classifications: {'peptide': 536}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 17, 'TRANS': 518}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 13
    Chain: "B"
      Number of atoms: 2956
      Number of conformers: 1
      Conformer: "A"
        Number of residues, atoms: 368, 2956
          Classifications: {'peptide': 368}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 1004
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 1004
          Classifications: {'peptide': 126}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 113}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 7
          Unusual residues: {' CA': 2, ' ZN': 1, 'ACT': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7743  SG  CYS C 289      37.781  59.224  44.747  1.00 57.24           S
  ATOM   7769  SG  CYS C 292      35.184  57.659  42.331  1.00 45.08           S
  ATOM   7952  SG  CYS C 315      38.825  56.578  42.087  1.00 59.56           S
  ATOM   7627  SG  CYS C 274      37.775  47.115  47.263  1.00 38.25           S
  ATOM   7651  SG  CYS C 277      37.170  43.505  48.360  1.00 48.40           S
  ATOM   7835  SG  CYS C 300      40.704  44.735  47.787  1.00 41.17           S

  Time building chain proxies: 5.20, per 1000 atoms: 0.62
  Number of scatterers: 8384
  At special positions: 0
  Unit cell: (122.094, 92.34, 109.782, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      3     29.99
     Ca      2     19.99
     S      55     16.00
     O    1548      8.00
     N    1447      7.00
     C    5329      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=0, symmetry=0
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 905.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 501 "
        pdb="ZN    ZN B 501 " - pdb=" ND1 HIS B 179 "
      pdb="  ZN C1101 "
        pdb="ZN    ZN C1101 " - pdb=" NE2 HIS C 318 "
        pdb="ZN    ZN C1101 " - pdb=" SG  CYS C 292 "
        pdb="ZN    ZN C1101 " - pdb=" SG  CYS C 315 "
        pdb="ZN    ZN C1101 " - pdb=" SG  CYS C 289 "
      pdb="  ZN C1102 "
        pdb="ZN    ZN C1102 " - pdb=" ND1 HIS C 297 "
        pdb="ZN    ZN C1102 " - pdb=" SG  CYS C 300 "
        pdb="ZN    ZN C1102 " - pdb=" SG  CYS C 277 "
        pdb="ZN    ZN C1102 " - pdb=" SG  CYS C 274 "
      Number of angles added : 6


  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1950

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      59.0% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 304 through 319
      removed outlier: 3.862A  pdb=" N   PHE A 308 " --> pdb=" O   THR A 304 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LYS A 319 " --> pdb=" O   ARG A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 336
    Processing helix  chain 'A' and resid 340 through 349
    Processing helix  chain 'A' and resid 355 through 367
    Processing helix  chain 'A' and resid 417 through 424
    Processing helix  chain 'A' and resid 446 through 484
      removed outlier: 3.795A  pdb=" N   GLU A 450 " --> pdb=" O   THR A 446 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLN A 451 " --> pdb=" O   PRO A 447 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LEU A 452 " --> pdb=" O   TYR A 448 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   LEU A 462 " --> pdb=" O   GLU A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 492
      removed outlier: 4.222A  pdb=" N   GLU A 492 " --> pdb=" O   PRO A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 517
    Processing helix  chain 'A' and resid 519 through 530
    Processing helix  chain 'A' and resid 530 through 561
      Proline residue:  A 536  - end of helix
    Processing helix  chain 'A' and resid 563 through 573
      removed outlier: 5.035A  pdb=" N   LEU A 569 " --> pdb=" O   GLU A 565 " (cutoff:3.500A)
      removed outlier: 5.205A  pdb=" N   LYS A 570 " --> pdb=" O   LYS A 566 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASP A 573 " --> pdb=" O   LEU A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 587
      removed outlier: 4.095A  pdb=" N   GLN A 581 " --> pdb=" O   VAL A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 610
      removed outlier: 3.557A  pdb=" N   ILE A 596 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   VAL A 599 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 643
      removed outlier: 3.626A  pdb=" N   LEU A 630 " --> pdb=" O   ASP A 626 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ARG A 643 " --> pdb=" O   TYR A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 661
    Processing helix  chain 'A' and resid 661 through 667
    Processing helix  chain 'A' and resid 746 through 786
      removed outlier: 3.652A  pdb=" N   LEU A 786 " --> pdb=" O   GLU A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 792
    Processing helix  chain 'A' and resid 808 through 829
      removed outlier: 5.040A  pdb=" N   TYR A 816 " --> pdb=" O   LEU A 812 " (cutoff:3.500A)
      Proline residue:  A 817  - end of helix
    Processing helix  chain 'A' and resid 832 through 845
    Processing helix  chain 'A' and resid 846 through 852
      removed outlier: 4.708A  pdb=" N   TYR A 849 " --> pdb=" O   ILE A 846 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A 850 " --> pdb=" O   HIS A 847 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 871
    Processing helix  chain 'A' and resid 871 through 887
      removed outlier: 3.530A  pdb=" N   LEU A 875 " --> pdb=" O   ASP A 871 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG A 887 " --> pdb=" O   ASN A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 915
      removed outlier: 5.412A  pdb=" N   ALA A 902 " --> pdb=" O   CYS A 898 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   ARG A 903 " --> pdb=" O   VAL A 899 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 23
      removed outlier: 3.725A  pdb=" N   TYR B  23 " --> pdb=" O   ILE B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 33 through 46
      removed outlier: 3.923A  pdb=" N   ARG B  37 " --> pdb=" O   PRO B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 66
    Processing helix  chain 'B' and resid 70 through 80
    Processing helix  chain 'B' and resid 81 through 87
      removed outlier: 4.114A  pdb=" N   MET B  85 " --> pdb=" O   PRO B  82 " (cutoff:3.500A)
      removed outlier: 5.621A  pdb=" N   SER B  86 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU B  87 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 95
    Processing helix  chain 'B' and resid 106 through 127
      removed outlier: 3.702A  pdb=" N   SER B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 165
      removed outlier: 3.582A  pdb=" N   LEU B 159 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 188
    Processing helix  chain 'B' and resid 217 through 221
    Processing helix  chain 'B' and resid 234 through 254
      removed outlier: 3.618A  pdb=" N   LYS B 243 " --> pdb=" O   GLY B 239 " (cutoff:3.500A)
      Proline residue:  B 244  - end of helix
    Processing helix  chain 'B' and resid 278 through 292
      removed outlier: 4.069A  pdb=" N   CYS B 285 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   VAL B 286 " --> pdb=" O   HIS B 282 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   PHE B 292 " --> pdb=" O   VAL B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 321
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 3.648A  pdb=" N   GLY B 339 " --> pdb=" O   GLU B 336 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 372
    Processing helix  chain 'C' and resid 20 through 28
    Processing helix  chain 'C' and resid 319 through 324
      removed outlier: 3.714A  pdb=" N   VAL C 323 " --> pdb=" O   ILE C 319 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 340
      removed outlier: 3.616A  pdb=" N   ARG C 334 " --> pdb=" O   THR C 330 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 347 through 360
    Processing sheet with id=AA1, first strand: chain 'A' and resid 396 through 397
      removed outlier: 3.718A  pdb=" N   ILE A 397 " --> pdb=" O   TYR A 401 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   TYR A 401 " --> pdb=" O   ILE A 397 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 620 through 624
      removed outlier: 4.314A  pdb=" N   VAL A 739 " --> pdb=" O   GLN A 927 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55
      removed outlier: 6.618A  pdb=" N   CYS B  13 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   ALA B 133 " --> pdb=" O   MET B 298 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   VAL B 258 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   LEU B 299 " --> pdb=" O   VAL B 258 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LEU B 260 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 259 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   GLN B 261 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   ILE B 174 " --> pdb=" O   GLN B 261 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   VAL B 171 " --> pdb=" O   MET B 195 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   VAL B 197 " --> pdb=" O   VAL B 171 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   TYR B 173 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   PHE B 199 " --> pdb=" O   TYR B 173 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   ASP B 175 " --> pdb=" O   PHE B 199 " (cutoff:3.500A)
      removed outlier: 8.663A  pdb=" N   LYS B 201 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
      removed outlier: 8.130A  pdb=" N   VAL B 225 " --> pdb=" O   VAL B 194 " (cutoff:3.500A)
      removed outlier: 6.181A  pdb=" N   THR B 196 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 7.685A  pdb=" N   PHE B 227 " --> pdb=" O   THR B 196 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   SER B 198 " --> pdb=" O   PHE B 227 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   MET B 229 " --> pdb=" O   SER B 198 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   HIS B 200 " --> pdb=" O   MET B 229 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 286 through 288

    425 hydrogen bonds defined for protein.
    1233 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 2.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2745
        1.34 -     1.46: 1962
        1.46 -     1.58: 3767
        1.58 -     1.71: 0
        1.71 -     1.83: 82
  Bond restraints: 8556
  Sorted by residual:
  bond pdb=" N   THR C  33 "
       pdb=" CA  THR C  33 "
    ideal  model  delta    sigma   weight residual
    1.455  1.491 -0.036 1.25e-02 6.40e+03 8.40e+00
  bond pdb=" N   LYS C  32 "
       pdb=" CA  LYS C  32 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.29e-02 6.01e+03 7.43e+00
  bond pdb=" N   CYS A 788 "
       pdb=" CA  CYS A 788 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.33e-02 5.65e+03 6.33e+00
  bond pdb=" C   PRO C  30 "
       pdb=" N   PRO C  31 "
    ideal  model  delta    sigma   weight residual
    1.335  1.368 -0.033 1.30e-02 5.92e+03 6.29e+00
  bond pdb=" N   LEU A 787 "
       pdb=" CA  LEU A 787 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.22e-02 6.72e+03 6.18e+00
  ... (remaining 8551 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 11358
        2.13 -     4.25: 164
        4.25 -     6.38: 19
        6.38 -     8.51: 3
        8.51 -    10.63: 1
  Bond angle restraints: 11545
  Sorted by residual:
  angle pdb=" O   PRO C  30 "
        pdb=" C   PRO C  30 "
        pdb=" N   PRO C  31 "
      ideal   model   delta    sigma   weight residual
     121.31  117.41    3.90 4.60e-01 4.73e+00 7.20e+01
  angle pdb=" CA  PRO C  30 "
        pdb=" C   PRO C  30 "
        pdb=" N   PRO C  31 "
      ideal   model   delta    sigma   weight residual
     117.73  121.74   -4.01 9.00e-01 1.23e+00 1.99e+01
  angle pdb=" C   GLU A 789 "
        pdb=" CA  GLU A 789 "
        pdb=" CB  GLU A 789 "
      ideal   model   delta    sigma   weight residual
     116.63  111.50    5.13 1.16e+00 7.43e-01 1.96e+01
  angle pdb=" N   CYS A 788 "
        pdb=" CA  CYS A 788 "
        pdb=" C   CYS A 788 "
      ideal   model   delta    sigma   weight residual
     113.28  108.13    5.15 1.22e+00 6.72e-01 1.78e+01
  angle pdb=" CA  GLU A 562 "
        pdb=" CB  GLU A 562 "
        pdb=" CG  GLU A 562 "
      ideal   model   delta    sigma   weight residual
     114.10  121.34   -7.24 2.00e+00 2.50e-01 1.31e+01
  ... (remaining 11540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 4418
       17.81 -    35.63: 528
       35.63 -    53.44: 184
       53.44 -    71.26: 33
       71.26 -    89.07: 12
  Dihedral angle restraints: 5175
    sinusoidal: 2151
      harmonic: 3024
  Sorted by residual:
  dihedral pdb=" CA  THR B 305 "
           pdb=" C   THR B 305 "
           pdb=" N   ILE B 306 "
           pdb=" CA  ILE B 306 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.69  -22.31     0      5.00e+00 4.00e-02 1.99e+01
  dihedral pdb=" CA  GLU A 562 "
           pdb=" C   GLU A 562 "
           pdb=" N   GLN A 563 "
           pdb=" CA  GLN A 563 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.50   20.50     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  TYR B 304 "
           pdb=" C   TYR B 304 "
           pdb=" N   THR B 305 "
           pdb=" CA  THR B 305 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.83   19.17     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 5172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 787
       0.034 -    0.067: 327
       0.067 -    0.101: 81
       0.101 -    0.135: 36
       0.135 -    0.168: 2
  Chirality restraints: 1233
  Sorted by residual:
  chirality pdb=" CA  LEU A 786 "
            pdb=" N   LEU A 786 "
            pdb=" C   LEU A 786 "
            pdb=" CB  LEU A 786 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.09e-01
  chirality pdb=" CA  GLU A 562 "
            pdb=" N   GLU A 562 "
            pdb=" C   GLU A 562 "
            pdb=" CB  GLU A 562 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.45e-01
  chirality pdb=" CA  VAL B 171 "
            pdb=" N   VAL B 171 "
            pdb=" C   VAL B 171 "
            pdb=" CB  VAL B 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.12e-01
  ... (remaining 1230 not shown)

  Planarity restraints: 1498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 269 "   -0.031 5.00e-02 4.00e+02   4.73e-02 3.59e+00
        pdb=" N   PRO C 270 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C 270 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 270 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B  39 "    0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   THR B  39 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   THR B  39 "    0.011 2.00e-02 2.50e+03
        pdb=" N   HIS B  40 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 864 "    0.008 2.00e-02 2.50e+03   1.53e-02 2.34e+00
        pdb=" C   GLN A 864 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   GLN A 864 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 865 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1495 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.38: 25
        2.38 -     3.01: 4713
        3.01 -     3.64: 12392
        3.64 -     4.27: 19083
        4.27 -     4.90: 31978
  Nonbonded interactions: 68191
  Sorted by model distance:
  nonbonded pdb=" O   ASN B  22 "
            pdb=" O   HOH B 601 "
     model   vdw
     1.755 3.040
  nonbonded pdb="ZN    ZN B 501 "
            pdb=" O   ACT B 504 "
     model   vdw
     1.878 2.230
  nonbonded pdb=" OD2 ASP B 265 "
            pdb="ZN    ZN B 501 "
     model   vdw
     1.918 2.230
  nonbonded pdb=" OD1 ASP B 177 "
            pdb="ZN    ZN B 501 "
     model   vdw
     1.947 2.230
  nonbonded pdb=" O   HOH A1204 "
            pdb=" O   HOH A1205 "
     model   vdw
     1.993 3.040
  ... (remaining 68186 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.570
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   8556  Z= 0.235
  Angle     :  0.614  10.634  11545  Z= 0.360
  Chirality :  0.041   0.168   1233
  Planarity :  0.004   0.047   1498
  Dihedral  : 17.771  89.069   3225
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.59 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1016
  helix:  1.17 (0.23), residues: 550
  sheet:  0.78 (0.62), residues: 76
  loop : -0.67 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 909 
 HIS   0.007   0.001   HIS A 867 
 PHE   0.012   0.001   PHE A 744 
 TYR   0.014   0.001   TYR B 304 
 ARG   0.004   0.000   ARG C 279 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  449 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7423 (mm-30)
REVERT: A  668 PHE cc_start: 0.4109 (OUTLIER) cc_final: 0.3499 (m-10)
  outliers start: 27
  outliers final: 21
  residues processed: 115
  average time/residue: 1.2069
  time to fit residues: 147.6973
Evaluate side-chains
  113 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  584 THR
Chi-restraints excluded: chain A residue  668 PHE
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  191 THR
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  349 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0040
   chunk 58 optimal weight:    0.7980
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.5192

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

Flipped N/Q/H residues before XYZ refinement:
A 582 ASN
A 756 HIS
B 226 ASN
C 321 HIS
C 328 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.170070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.132503 restraints weight = 10062.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 1.66
r_work: 0.3331 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.0772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   8556  Z= 0.158
  Angle     :  0.512   6.840  11545  Z= 0.273
  Chirality :  0.039   0.150   1233
  Planarity :  0.004   0.042   1498
  Dihedral  :  6.226  55.208   1165
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 22.83 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.27), residues: 1016
  helix:  1.74 (0.22), residues: 564
  sheet:  0.95 (0.63), residues: 76
  loop : -0.60 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 749 
 HIS   0.006   0.001   HIS A 867 
 PHE   0.009   0.001   PHE A 662 
 TYR   0.013   0.001   TYR B 304 
 ARG   0.003   0.000   ARG A 627 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 99
  time to evaluate  : 0.850 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 PHE cc_start: 0.7307 (t80) cc_final: 0.7021 (t80)
REVERT: A  449 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7335 (mm-30)
REVERT: A  668 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.3923 (m-10)
REVERT: A  842 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7669 (pt0)
REVERT: A  865 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7465 (mt)
REVERT: A  867 HIS cc_start: 0.7120 (t70) cc_final: 0.6646 (t70)
REVERT: A  927 GLN cc_start: 0.6220 (tt0) cc_final: 0.5574 (mp10)
REVERT: A  937 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8074 (pt0)
REVERT: C  302 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7177 (mm-30)
  outliers start: 36
  outliers final: 21
  residues processed: 126
  average time/residue: 1.2762
  time to fit residues: 170.8724
Evaluate side-chains
  117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  584 THR
Chi-restraints excluded: chain A residue  668 PHE
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   87 GLU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain C residue  323 VAL
Chi-restraints excluded: chain C residue  347 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 79 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 81 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0040
   chunk 6 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 56 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9990
   overall best weight:    0.6398

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

Flipped N/Q/H residues before XYZ refinement:
C 321 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.170873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.132823 restraints weight = 10087.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 1.69
r_work: 0.3332 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3209 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3192
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3192 r_free = 0.3192    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3192
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.0996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8556  Z= 0.154
  Angle     :  0.486   7.626  11545  Z= 0.257
  Chirality :  0.038   0.142   1233
  Planarity :  0.003   0.037   1498
  Dihedral  :  5.576  55.163   1155
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.94 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.27), residues: 1016
  helix:  1.94 (0.22), residues: 564
  sheet:  1.03 (0.63), residues: 76
  loop : -0.58 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 749 
 HIS   0.006   0.001   HIS A 867 
 PHE   0.009   0.001   PHE A 744 
 TYR   0.012   0.001   TYR B 304 
 ARG   0.003   0.000   ARG B 127 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.950 
Fit side-chains
REVERT: A  327 PHE cc_start: 0.7280 (t80) cc_final: 0.6985 (t80)
REVERT: A  668 PHE cc_start: 0.4316 (OUTLIER) cc_final: 0.3817 (m-10)
REVERT: A  842 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7681 (pt0)
REVERT: A  865 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7548 (mt)
REVERT: A  880 LEU cc_start: 0.6387 (mt) cc_final: 0.6162 (tp)
REVERT: A  913 ARG cc_start: 0.3348 (OUTLIER) cc_final: 0.3108 (tmm160)
REVERT: A  927 GLN cc_start: 0.6203 (tt0) cc_final: 0.5573 (mp10)
REVERT: B  236 GLU cc_start: 0.7197 (pm20) cc_final: 0.6980 (pm20)
REVERT: C  302 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.7167 (mm-30)
  outliers start: 38
  outliers final: 16
  residues processed: 130
  average time/residue: 1.4167
  time to fit residues: 195.6692
Evaluate side-chains
  111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  668 PHE
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0020
   chunk 57 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 321 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.170490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.132689 restraints weight = 9882.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.70
r_work: 0.3328 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3206 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.1104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8556  Z= 0.170
  Angle     :  0.495   7.850  11545  Z= 0.260
  Chirality :  0.039   0.137   1233
  Planarity :  0.003   0.036   1498
  Dihedral  :  5.363  56.615   1149
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.16 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.27), residues: 1016
  helix:  1.96 (0.22), residues: 564
  sheet:  1.01 (0.63), residues: 76
  loop : -0.64 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 749 
 HIS   0.014   0.001   HIS C 318 
 PHE   0.009   0.001   PHE A 744 
 TYR   0.012   0.001   TYR B 304 
 ARG   0.002   0.000   ARG A 396 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 97
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
REVERT: A  450 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7037 (mm-30)
REVERT: A  668 PHE cc_start: 0.4246 (OUTLIER) cc_final: 0.3779 (m-10)
REVERT: A  842 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7656 (pt0)
REVERT: A  865 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7584 (mt)
REVERT: A  880 LEU cc_start: 0.6427 (mt) cc_final: 0.6156 (tp)
REVERT: A  927 GLN cc_start: 0.6290 (tt0) cc_final: 0.5576 (mp10)
REVERT: A  937 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7909 (pt0)
REVERT: C  302 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7146 (mm-30)
  outliers start: 38
  outliers final: 18
  residues processed: 129
  average time/residue: 1.4419
  time to fit residues: 198.2612
Evaluate side-chains
  111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  668 PHE
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain C residue  347 GLN
Chi-restraints excluded: chain C residue  349 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 582 ASN
C 321 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.169914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.131721 restraints weight = 9934.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 1.66
r_work: 0.3324 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3202 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.1199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8556  Z= 0.173
  Angle     :  0.493   8.166  11545  Z= 0.259
  Chirality :  0.039   0.133   1233
  Planarity :  0.003   0.038   1498
  Dihedral  :  5.365  57.938   1149
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.50 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.53 (0.27), residues: 1016
  helix:  2.10 (0.22), residues: 553
  sheet:  1.00 (0.63), residues: 76
  loop : -0.59 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 749 
 HIS   0.006   0.001   HIS A 867 
 PHE   0.009   0.001   PHE B 335 
 TYR   0.011   0.001   TYR B 304 
 ARG   0.003   0.000   ARG B 127 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 96
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
REVERT: A  327 PHE cc_start: 0.7248 (t80) cc_final: 0.6901 (t80)
REVERT: A  450 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7094 (mm-30)
REVERT: A  631 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6581 (mp0)
REVERT: A  668 PHE cc_start: 0.4287 (OUTLIER) cc_final: 0.3784 (m-10)
REVERT: A  842 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7652 (pt0)
REVERT: A  865 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7599 (mt)
REVERT: A  880 LEU cc_start: 0.6459 (mt) cc_final: 0.6196 (tp)
REVERT: A  927 GLN cc_start: 0.6215 (tt0) cc_final: 0.5530 (mp10)
REVERT: A  937 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7889 (pt0)
REVERT: B  236 GLU cc_start: 0.7292 (pm20) cc_final: 0.7063 (pm20)
REVERT: C  302 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7161 (mm-30)
  outliers start: 42
  outliers final: 21
  residues processed: 131
  average time/residue: 1.4642
  time to fit residues: 203.5693
Evaluate side-chains
  119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  631 GLU
Chi-restraints excluded: chain A residue  668 PHE
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  845 THR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  231 ASP
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain C residue  347 GLN
Chi-restraints excluded: chain C residue  349 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 23 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0970
   chunk 16 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 931 GLN
B  34 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.169374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.131045 restraints weight = 9855.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.63
r_work: 0.3317 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3180
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3180 r_free = 0.3180    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3180
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8556  Z= 0.195
  Angle     :  0.510   8.629  11545  Z= 0.268
  Chirality :  0.039   0.129   1233
  Planarity :  0.003   0.039   1498
  Dihedral  :  5.458  57.776   1149
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 23.71 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.27), residues: 1016
  helix:  1.99 (0.22), residues: 559
  sheet:  0.97 (0.64), residues: 76
  loop : -0.72 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 749 
 HIS   0.007   0.001   HIS A 867 
 PHE   0.010   0.001   PHE A 744 
 TYR   0.013   0.001   TYR B 304 
 ARG   0.002   0.000   ARG C 334 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 97
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
REVERT: A  319 LYS cc_start: 0.6984 (mmmt) cc_final: 0.6724 (mmmm)
REVERT: A  450 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7111 (mm-30)
REVERT: A  668 PHE cc_start: 0.4235 (OUTLIER) cc_final: 0.3764 (m-10)
REVERT: A  842 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7636 (pt0)
REVERT: A  865 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7773 (mt)
REVERT: A  927 GLN cc_start: 0.6206 (tt0) cc_final: 0.5472 (mp10)
REVERT: A  937 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7841 (pt0)
REVERT: C  302 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7137 (mm-30)
REVERT: C  308 MET cc_start: 0.7777 (mmt) cc_final: 0.7518 (tpp)
  outliers start: 41
  outliers final: 23
  residues processed: 129
  average time/residue: 1.3276
  time to fit residues: 182.2773
Evaluate side-chains
  123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  668 PHE
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  845 THR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  865 LEU
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  347 GLN
Chi-restraints excluded: chain C residue  349 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0670
   chunk 21 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0010
   chunk 79 optimal weight:    0.0040
   chunk 89 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
B 354 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.171702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.134248 restraints weight = 10037.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.77
r_work: 0.3346 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3209
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3209 r_free = 0.3209    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3209
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8556  Z= 0.131
  Angle     :  0.473   8.686  11545  Z= 0.248
  Chirality :  0.038   0.128   1233
  Planarity :  0.003   0.038   1498
  Dihedral  :  5.273  58.877   1149
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 24.26 %
    Favored  : 72.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.27), residues: 1016
  helix:  2.13 (0.22), residues: 560
  sheet:  1.02 (0.64), residues: 76
  loop : -0.60 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 749 
 HIS   0.006   0.001   HIS C 318 
 PHE   0.009   0.001   PHE A 334 
 TYR   0.012   0.001   TYR B 304 
 ARG   0.004   0.000   ARG B 127 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 97
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
REVERT: A  319 LYS cc_start: 0.6976 (mmmt) cc_final: 0.6596 (mmmm)
REVERT: A  327 PHE cc_start: 0.7137 (t80) cc_final: 0.6805 (t80)
REVERT: A  354 LYS cc_start: 0.3940 (OUTLIER) cc_final: 0.3371 (ttmm)
REVERT: A  450 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7079 (mm-30)
REVERT: A  457 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7292 (m-30)
REVERT: A  842 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7629 (pt0)
REVERT: A  880 LEU cc_start: 0.6438 (mt) cc_final: 0.6164 (tp)
REVERT: A  927 GLN cc_start: 0.6294 (tt0) cc_final: 0.5608 (mp10)
REVERT: A  937 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7789 (pt0)
REVERT: B   67 LYS cc_start: 0.8449 (OUTLIER) cc_final: 0.8169 (mttm)
REVERT: C  302 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7132 (mm-30)
REVERT: C  308 MET cc_start: 0.7737 (mmt) cc_final: 0.7443 (tpp)
REVERT: C  315 CYS cc_start: 0.6659 (p) cc_final: 0.6376 (p)
  outliers start: 32
  outliers final: 15
  residues processed: 121
  average time/residue: 1.3589
  time to fit residues: 174.1290
Evaluate side-chains
  116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  845 THR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   67 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain C residue  347 GLN
Chi-restraints excluded: chain C residue  349 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 27 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.168531 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.127025 restraints weight = 10139.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.69
r_work: 0.3308 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8556  Z= 0.233
  Angle     :  0.537   8.883  11545  Z= 0.282
  Chirality :  0.040   0.118   1233
  Planarity :  0.004   0.038   1498
  Dihedral  :  5.454  58.106   1147
  Min Nonbonded Distance : 1.934

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.49 %
    Favored  : 72.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1016
  helix:  1.93 (0.22), residues: 561
  sheet:  0.90 (0.64), residues: 76
  loop : -0.72 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 749 
 HIS   0.008   0.001   HIS A 867 
 PHE   0.013   0.001   PHE A 744 
 TYR   0.015   0.002   TYR B 304 
 ARG   0.006   0.000   ARG C 279 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 92
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
REVERT: A  319 LYS cc_start: 0.7004 (mmmt) cc_final: 0.6747 (mmmm)
REVERT: A  327 PHE cc_start: 0.7154 (t80) cc_final: 0.6816 (t80)
REVERT: A  354 LYS cc_start: 0.4236 (OUTLIER) cc_final: 0.3438 (ttmm)
REVERT: A  450 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7137 (mm-30)
REVERT: A  668 PHE cc_start: 0.4197 (OUTLIER) cc_final: 0.3713 (m-10)
REVERT: A  842 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7759 (pt0)
REVERT: A  927 GLN cc_start: 0.6238 (tt0) cc_final: 0.5505 (mp10)
REVERT: A  937 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7831 (pt0)
REVERT: B   38 MET cc_start: 0.8849 (mtp) cc_final: 0.8619 (mtm)
REVERT: B   67 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8248 (mttm)
REVERT: B  250 MET cc_start: 0.8639 (mmt) cc_final: 0.8401 (mmt)
REVERT: C  302 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7195 (mm-30)
REVERT: C  308 MET cc_start: 0.7924 (mmt) cc_final: 0.7668 (tpp)
  outliers start: 37
  outliers final: 23
  residues processed: 122
  average time/residue: 1.6987
  time to fit residues: 219.7880
Evaluate side-chains
  122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 92
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  359 PHE
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  668 PHE
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  845 THR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   67 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain B residue  352 THR
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  347 GLN
Chi-restraints excluded: chain C residue  349 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 85 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 87 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  34 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.169575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.131161 restraints weight = 10195.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 1.73
r_work: 0.3314 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3178
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3178 r_free = 0.3178    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3178
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8556  Z= 0.174
  Angle     :  0.502   9.544  11545  Z= 0.264
  Chirality :  0.039   0.117   1233
  Planarity :  0.003   0.037   1498
  Dihedral  :  5.415  58.673   1147
  Min Nonbonded Distance : 1.963

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 23.93 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1016
  helix:  2.06 (0.22), residues: 555
  sheet:  0.87 (0.63), residues: 76
  loop : -0.66 (0.30), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 749 
 HIS   0.006   0.001   HIS A 867 
 PHE   0.036   0.001   PHE A 334 
 TYR   0.013   0.001   TYR B 304 
 ARG   0.008   0.000   ARG C 279 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: A  319 LYS cc_start: 0.6978 (mmmt) cc_final: 0.6724 (mmmm)
REVERT: A  327 PHE cc_start: 0.7102 (t80) cc_final: 0.6764 (t80)
REVERT: A  354 LYS cc_start: 0.4146 (OUTLIER) cc_final: 0.3379 (ttmm)
REVERT: A  450 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7128 (mm-30)
REVERT: A  668 PHE cc_start: 0.4357 (OUTLIER) cc_final: 0.3880 (m-10)
REVERT: A  842 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7628 (pt0)
REVERT: A  927 GLN cc_start: 0.6203 (tt0) cc_final: 0.5481 (mp10)
REVERT: A  937 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7835 (pt0)
REVERT: B   38 MET cc_start: 0.8771 (mtp) cc_final: 0.8558 (mtm)
REVERT: B   67 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8205 (mttm)
REVERT: C  302 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7215 (mm-30)
REVERT: C  308 MET cc_start: 0.7905 (mmt) cc_final: 0.7640 (tpp)
  outliers start: 32
  outliers final: 19
  residues processed: 118
  average time/residue: 1.3707
  time to fit residues: 171.3144
Evaluate side-chains
  119 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.756 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  668 PHE
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  845 THR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   67 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  347 GLN
Chi-restraints excluded: chain C residue  349 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 7 optimal weight:    0.2980
   chunk 78 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3983 r_free = 0.3983 target = 0.170005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.129040 restraints weight = 10059.592|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.80
r_work: 0.3325 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3181
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8556  Z= 0.176
  Angle     :  0.513   9.943  11545  Z= 0.270
  Chirality :  0.039   0.146   1233
  Planarity :  0.003   0.038   1498
  Dihedral  :  5.422  58.900   1147
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 24.37 %
    Favored  : 72.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.26), residues: 1016
  helix:  2.06 (0.22), residues: 556
  sheet:  0.90 (0.63), residues: 76
  loop : -0.66 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 749 
 HIS   0.005   0.001   HIS A 867 
 PHE   0.009   0.001   PHE A 744 
 TYR   0.013   0.001   TYR B 304 
 ARG   0.008   0.000   ARG C 279 

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

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

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2032 Ramachandran restraints generated.
    1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
REVERT: A  319 LYS cc_start: 0.7003 (mmmt) cc_final: 0.6750 (mmmm)
REVERT: A  327 PHE cc_start: 0.7180 (t80) cc_final: 0.6818 (t80)
REVERT: A  354 LYS cc_start: 0.4150 (OUTLIER) cc_final: 0.3393 (ttmm)
REVERT: A  450 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7140 (mm-30)
REVERT: A  457 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7349 (m-30)
REVERT: A  668 PHE cc_start: 0.4375 (OUTLIER) cc_final: 0.3899 (m-10)
REVERT: A  842 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7749 (pt0)
REVERT: A  927 GLN cc_start: 0.6241 (tt0) cc_final: 0.5556 (mp10)
REVERT: A  937 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7820 (pt0)
REVERT: B   38 MET cc_start: 0.8694 (mtp) cc_final: 0.8478 (mtm)
REVERT: B   67 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8231 (mttm)
REVERT: C  302 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7236 (mm-30)
REVERT: C  308 MET cc_start: 0.7932 (mmt) cc_final: 0.7677 (tpp)
REVERT: C  314 MET cc_start: 0.6955 (ttt) cc_final: 0.6735 (ttt)
  outliers start: 28
  outliers final: 19
  residues processed: 117
  average time/residue: 1.3381
  time to fit residues: 165.9375
Evaluate side-chains
  121 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  354 LYS
Chi-restraints excluded: chain A residue  450 GLU
Chi-restraints excluded: chain A residue  457 ASP
Chi-restraints excluded: chain A residue  483 LEU
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  668 PHE
Chi-restraints excluded: chain A residue  842 GLU
Chi-restraints excluded: chain A residue  845 THR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  873 VAL
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   67 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  291 THR
Chi-restraints excluded: chain C residue  287 ILE
Chi-restraints excluded: chain C residue  302 GLU
Chi-restraints excluded: chain C residue  310 LEU
Chi-restraints excluded: chain C residue  319 ILE
Chi-restraints excluded: chain C residue  341 PHE
Chi-restraints excluded: chain C residue  347 GLN
Chi-restraints excluded: chain C residue  349 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 62 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0030
   chunk 100 optimal weight:    4.9990
   chunk 35 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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 = 0.3985 r_free = 0.3985 target = 0.170226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.129321 restraints weight = 10133.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.85
r_work: 0.3327 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3195
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3195 r_free = 0.3195    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3195
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.1590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8556  Z= 0.165
  Angle     :  0.501   9.720  11545  Z= 0.263
  Chirality :  0.039   0.123   1233
  Planarity :  0.003   0.037   1498
  Dihedral  :  5.425  59.022   1147
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 24.15 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.27), residues: 1016
  helix:  2.05 (0.22), residues: 561
  sheet:  0.93 (0.64), residues: 76
  loop : -0.72 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 909 
 HIS   0.005   0.001   HIS A 867 
 PHE   0.036   0.001   PHE A 334 
 TYR   0.012   0.001   TYR B 304 
 ARG   0.008   0.000   ARG C 279 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7722.75 seconds
wall clock time: 136 minutes 21.36 seconds (8181.36 seconds total)