Starting phenix.real_space_refine
on Wed Feb 12 23:08:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bpc_16149/02_2025/8bpc_16149_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bpc_16149/02_2025/8bpc_16149.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/8bpc_16149/02_2025/8bpc_16149.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bpc_16149/02_2025/8bpc_16149.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bpc_16149/02_2025/8bpc_16149_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bpc_16149/02_2025/8bpc_16149_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=   0.003
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    5342      2.51       5
     N    1449      2.21       5
     O    1582      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8433
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 4405
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4405
          Classifications: {'peptide': 536}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 17, 'TRANS': 518}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          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: 22
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 22
          Unusual residues: {' CA': 2, ' ZN': 1, 'SHH': 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: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 39
          Classifications: {'water': 39}
          Link IDs: {None: 38}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7745  SG  CYS C 289      37.812  59.778  45.110  1.00 57.24           S
  ATOM   7771  SG  CYS C 292      35.245  58.180  42.684  1.00 45.08           S
  ATOM   7954  SG  CYS C 315      38.906  57.170  42.432  1.00 59.56           S
  ATOM   7629  SG  CYS C 274      38.038  47.655  47.545  1.00 38.25           S
  ATOM   7653  SG  CYS C 277      37.502  44.027  48.618  1.00 48.40           S
  ATOM   7837  SG  CYS C 300      41.011  45.328  48.053  1.00 41.17           S

  Time building chain proxies: 5.13, per 1000 atoms: 0.61
  Number of scatterers: 8433
  At special positions: 0
  Unit cell: (121.92, 93.472, 110.744, 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    1582      8.00
     N    1449      7.00
     C    5342      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: 2.28
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 502 "
        pdb="ZN    ZN B 502 " - pdb=" ND1 HIS B 179 "
      pdb="  ZN C 401 "
        pdb="ZN    ZN C 401 " - pdb=" NE2 HIS C 318 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 292 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 315 "
        pdb="ZN    ZN C 401 " - pdb=" SG  CYS C 289 "
      pdb="  ZN C 402 "
        pdb="ZN    ZN C 402 " - pdb=" ND1 HIS C 297 "
        pdb="ZN    ZN C 402 " - pdb=" SG  CYS C 300 "
        pdb="ZN    ZN C 402 " - pdb=" SG  CYS C 277 "
        pdb="ZN    ZN C 402 " - 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:
      44 helices and 4 sheets defined
      59.5% alpha, 6.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 304 through 319
      removed outlier: 3.861A  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 441 through 445
      removed outlier: 3.548A  pdb=" N   LYS A 445 " --> pdb=" O   SER A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 484
      removed outlier: 3.647A  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: 3.556A  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: 3.651A  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: 3.594A  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: 5.831A  pdb=" N   ARG A 903 " --> pdb=" O   VAL A 899 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 23
      removed outlier: 3.726A  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: 5.620A  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: 3.703A  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: 4.070A  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: 6.435A  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: 7.938A  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: 7.795A  pdb=" N   GLN B 261 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ILE B 174 " --> pdb=" O   GLN B 261 " (cutoff:3.500A)
      removed outlier: 6.856A  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: 6.450A  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: 7.794A  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

    428 hydrogen bonds defined for protein.
    1239 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: 2.42

  Time building geometry restraints manager: 2.52 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2156
        1.33 -     1.46: 1852
        1.46 -     1.58: 4484
        1.58 -     1.70: 0
        1.70 -     1.83: 82
  Bond restraints: 8574
  Sorted by residual:
  bond pdb=" CA  SER A 430 "
       pdb=" CB  SER A 430 "
    ideal  model  delta    sigma   weight residual
    1.529  1.485  0.044 1.34e-02 5.57e+03 1.08e+01
  bond pdb=" N   THR A 446 "
       pdb=" CA  THR A 446 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.14e-02 7.69e+03 8.99e+00
  bond pdb=" N   TRP A 434 "
       pdb=" CA  TRP A 434 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.034 1.16e-02 7.43e+03 8.80e+00
  bond pdb=" N   VAL A 429 "
       pdb=" CA  VAL A 429 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.19e-02 7.06e+03 7.82e+00
  bond pdb=" N   LYS B  11 "
       pdb=" CA  LYS B  11 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.033 1.21e-02 6.83e+03 7.44e+00
  ... (remaining 8569 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 11317
        2.13 -     4.26: 214
        4.26 -     6.39: 31
        6.39 -     8.52: 3
        8.52 -    10.65: 2
  Bond angle restraints: 11567
  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  117.73    3.58 4.60e-01 4.73e+00 6.06e+01
  angle pdb=" C   THR A 427 "
        pdb=" N   TRP A 428 "
        pdb=" CA  TRP A 428 "
      ideal   model   delta    sigma   weight residual
     122.64  112.99    9.65 1.70e+00 3.46e-01 3.22e+01
  angle pdb=" N   PRO C  31 "
        pdb=" CA  PRO C  31 "
        pdb=" CB  PRO C  31 "
      ideal   model   delta    sigma   weight residual
     102.35  105.94   -3.59 7.10e-01 1.98e+00 2.56e+01
  angle pdb=" C   VAL A 429 "
        pdb=" N   SER A 430 "
        pdb=" CA  SER A 430 "
      ideal   model   delta    sigma   weight residual
     122.77  116.84    5.93 1.33e+00 5.65e-01 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  111.48    5.15 1.16e+00 7.43e-01 1.97e+01
  ... (remaining 11562 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 4429
       17.83 -    35.66: 528
       35.66 -    53.49: 185
       53.49 -    71.31: 30
       71.31 -    89.14: 11
  Dihedral angle restraints: 5183
    sinusoidal: 2159
      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 -157.68  -22.32     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  160.87   19.13     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 5180 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1116
       0.071 -    0.142: 110
       0.142 -    0.213: 5
       0.213 -    0.284: 1
       0.284 -    0.355: 2
  Chirality restraints: 1234
  Sorted by residual:
  chirality pdb=" CB  VAL B  12 "
            pdb=" CA  VAL B  12 "
            pdb=" CG1 VAL B  12 "
            pdb=" CG2 VAL B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.27   -0.35 2.00e-01 2.50e+01 3.15e+00
  chirality pdb=" CB  VAL A 441 "
            pdb=" CA  VAL A 441 "
            pdb=" CG1 VAL A 441 "
            pdb=" CG2 VAL A 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.32 2.00e-01 2.50e+01 2.64e+00
  chirality pdb=" CB  VAL A 429 "
            pdb=" CA  VAL A 429 "
            pdb=" CG1 VAL A 429 "
            pdb=" CG2 VAL A 429 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.83e+00
  ... (remaining 1231 not shown)

  Planarity restraints: 1500
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 SHH B 501 "    0.008 2.00e-02 2.50e+03   1.91e-02 6.40e+00
        pdb=" C11 SHH B 501 "   -0.012 2.00e-02 2.50e+03
        pdb=" C12 SHH B 501 "   -0.007 2.00e-02 2.50e+03
        pdb=" C13 SHH B 501 "    0.001 2.00e-02 2.50e+03
        pdb=" C14 SHH B 501 "   -0.004 2.00e-02 2.50e+03
        pdb=" C9  SHH B 501 "    0.040 2.00e-02 2.50e+03
        pdb=" N2  SHH B 501 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 269 "   -0.031 5.00e-02 4.00e+02   4.74e-02 3.60e+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=" C7  SHH B 501 "   -0.015 2.00e-02 2.50e+03   1.57e-02 3.09e+00
        pdb=" C8  SHH B 501 "    0.008 2.00e-02 2.50e+03
        pdb=" C9  SHH B 501 "   -0.019 2.00e-02 2.50e+03
        pdb=" N2  SHH B 501 "    0.024 2.00e-02 2.50e+03
        pdb=" O3  SHH B 501 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1497 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.23: 12
        2.23 -     2.89: 3249
        2.89 -     3.56: 11985
        3.56 -     4.23: 19656
        4.23 -     4.90: 34082
  Nonbonded interactions: 68984
  Sorted by model distance:
  nonbonded pdb=" O   HOH B 608 "
            pdb=" O   HOH B 632 "
     model   vdw
     1.557 3.040
  nonbonded pdb=" OH  TYR B  16 "
            pdb=" O   HOH B 601 "
     model   vdw
     1.648 3.040
  nonbonded pdb=" OE2 GLU A 461 "
            pdb=" O   HOH A1201 "
     model   vdw
     1.815 3.040
  nonbonded pdb=" OD2 ASP B 265 "
            pdb="ZN    ZN B 502 "
     model   vdw
     1.919 2.230
  nonbonded pdb=" OD1 ASP B 177 "
            pdb="ZN    ZN B 502 "
     model   vdw
     1.946 2.230
  ... (remaining 68979 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:             1.080
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     23.050
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
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   0.065   8574  Z= 0.268
  Angle     :  0.686  10.650  11567  Z= 0.411
  Chirality :  0.045   0.355   1234
  Planarity :  0.004   0.047   1500
  Dihedral  : 17.594  89.143   3233
  Min Nonbonded Distance : 1.557

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 24.34 %
    Favored  : 72.48 %
  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:  0.55 (0.27), residues: 1016
  helix:  1.13 (0.23), residues: 551
  sheet:  0.60 (0.62), residues: 76
  loop : -0.73 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 434 
 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 A 495 

*********************** 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
  218 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 189
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  328 LEU cc_start: 0.6042 (OUTLIER) cc_final: 0.5659 (mp)
REVERT: A  395 LYS cc_start: 0.3960 (mttt) cc_final: 0.3599 (ttpt)
REVERT: A  486 MET cc_start: 0.6555 (ptt) cc_final: 0.6302 (ptp)
REVERT: C   21 MET cc_start: 0.8165 (tpp) cc_final: 0.7847 (tpt)
  outliers start: 29
  outliers final: 5
  residues processed: 210
  average time/residue: 1.4158
  time to fit residues: 313.7206
Evaluate side-chains
  106 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  328 LEU
Chi-restraints excluded: chain A residue  877 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  319 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    9.9990
   chunk 58 optimal weight:    0.8980
   chunk 91 optimal weight:    9.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 582 ASN
A 773 GLN
A 919 ASN
B  22 ASN
B  58 HIS
B  96 ASN
B 226 ASN
C 288 GLN
C 328 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.165053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.118561 restraints weight = 10707.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 1.94
r_work: 0.3289 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3150
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3150 r_free = 0.3150    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   8574  Z= 0.333
  Angle     :  0.652  12.316  11567  Z= 0.339
  Chirality :  0.045   0.193   1234
  Planarity :  0.005   0.049   1500
  Dihedral  :  5.195  50.741   1148
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  6.47 %
    Allowed  : 20.29 %
    Favored  : 73.25 %
  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:  0.67 (0.26), residues: 1016
  helix:  1.30 (0.22), residues: 559
  sheet:  0.77 (0.63), residues: 74
  loop : -0.87 (0.31), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 560 
 HIS   0.010   0.002   HIS A 867 
 PHE   0.017   0.002   PHE A 662 
 TYR   0.020   0.002   TYR B 304 
 ARG   0.022   0.001   ARG B 127 

*********************** 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
  168 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 109
  time to evaluate  : 1.203 
Fit side-chains
REVERT: A  342 SER cc_start: 0.3624 (OUTLIER) cc_final: 0.3103 (m)
REVERT: A  395 LYS cc_start: 0.3749 (mttt) cc_final: 0.3071 (ttmt)
REVERT: A  476 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8460 (mp)
REVERT: A  486 MET cc_start: 0.7512 (ptt) cc_final: 0.6770 (ptp)
REVERT: A  493 LYS cc_start: 0.7889 (mmmm) cc_final: 0.7454 (ptpt)
REVERT: A  631 GLU cc_start: 0.7712 (pt0) cc_final: 0.7202 (tp30)
REVERT: A  743 PHE cc_start: 0.8062 (t80) cc_final: 0.7749 (t80)
REVERT: A  813 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7425 (pt0)
REVERT: A  868 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7536 (mp)
REVERT: A  875 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.7007 (mt)
REVERT: A  876 LYS cc_start: 0.7316 (tttt) cc_final: 0.6918 (tttt)
REVERT: A  913 ARG cc_start: 0.4334 (OUTLIER) cc_final: 0.3928 (ptm160)
REVERT: B   44 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8369 (mp)
REVERT: B   63 GLU cc_start: 0.8431 (mp0) cc_final: 0.8160 (mp0)
REVERT: B   75 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8034 (tttt)
REVERT: B  128 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8166 (mt0)
REVERT: B  358 GLU cc_start: 0.8408 (pm20) cc_final: 0.7975 (tt0)
  outliers start: 59
  outliers final: 15
  residues processed: 152
  average time/residue: 1.4812
  time to fit residues: 237.9333
Evaluate side-chains
  104 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  813 GLU
Chi-restraints excluded: chain A residue  868 LEU
Chi-restraints excluded: chain A residue  875 LEU
Chi-restraints excluded: chain A residue  878 VAL
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   44 LEU
Chi-restraints excluded: chain B residue   52 MET
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  114 SER
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain B residue  369 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 3 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 54 optimal weight:    0.2980
   chunk 72 optimal weight:    0.3980
   chunk 65 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 578 ASN
A 582 ASN
A 603 HIS
B  58 HIS
C 288 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.167864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.122250 restraints weight = 10906.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 1.90
r_work: 0.3331 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8574  Z= 0.167
  Angle     :  0.503   7.463  11567  Z= 0.268
  Chirality :  0.039   0.154   1234
  Planarity :  0.004   0.039   1500
  Dihedral  :  4.482  32.467   1144
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 22.92 %
    Favored  : 73.25 %
  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:  1.12 (0.27), residues: 1016
  helix:  1.71 (0.22), residues: 561
  sheet:  0.79 (0.63), residues: 76
  loop : -0.73 (0.31), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 434 
 HIS   0.005   0.001   HIS C 348 
 PHE   0.014   0.001   PHE A 662 
 TYR   0.021   0.001   TYR A 740 
 ARG   0.005   0.000   ARG A 928 

*********************** 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
  129 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 94
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  342 SER cc_start: 0.3193 (OUTLIER) cc_final: 0.2635 (m)
REVERT: A  347 LEU cc_start: 0.6083 (mt) cc_final: 0.5851 (tt)
REVERT: A  486 MET cc_start: 0.7371 (ptt) cc_final: 0.6757 (ptp)
REVERT: A  493 LYS cc_start: 0.7869 (mmmm) cc_final: 0.7426 (ptpt)
REVERT: A  530 ASN cc_start: 0.7557 (p0) cc_final: 0.7310 (p0)
REVERT: A  813 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7274 (pp20)
REVERT: A  913 ARG cc_start: 0.4647 (OUTLIER) cc_final: 0.4263 (ptm160)
REVERT: B   63 GLU cc_start: 0.8412 (mp0) cc_final: 0.8164 (mp0)
REVERT: B   75 LYS cc_start: 0.8612 (OUTLIER) cc_final: 0.8164 (tttt)
REVERT: B  358 GLU cc_start: 0.8508 (pm20) cc_final: 0.8005 (tt0)
REVERT: C   23 GLN cc_start: 0.7478 (mt0) cc_final: 0.7194 (mt0)
REVERT: C  288 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7676 (tp-100)
  outliers start: 35
  outliers final: 12
  residues processed: 117
  average time/residue: 1.3090
  time to fit residues: 162.9172
Evaluate side-chains
  100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  813 GLU
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  350 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0980
   chunk 17 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 425 ASN
A 603 HIS
A 756 HIS
B  40 HIS
B  58 HIS
C 288 GLN
** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 321 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.165394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.119635 restraints weight = 10836.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.92
r_work: 0.3299 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.4100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8574  Z= 0.178
  Angle     :  0.502   6.289  11567  Z= 0.264
  Chirality :  0.039   0.158   1234
  Planarity :  0.004   0.048   1500
  Dihedral  :  4.415  31.377   1144
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.25 %
    Favored  : 73.36 %
  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:  1.25 (0.27), residues: 1016
  helix:  1.84 (0.22), residues: 561
  sheet:  0.81 (0.64), residues: 76
  loop : -0.70 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 434 
 HIS   0.008   0.001   HIS C 318 
 PHE   0.014   0.001   PHE A 662 
 TYR   0.016   0.001   TYR B 304 
 ARG   0.010   0.000   ARG A 863 

*********************** 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
  118 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 87
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A  342 SER cc_start: 0.3002 (OUTLIER) cc_final: 0.2480 (m)
REVERT: A  347 LEU cc_start: 0.6014 (mt) cc_final: 0.5799 (tt)
REVERT: A  486 MET cc_start: 0.7558 (ptt) cc_final: 0.6986 (ptp)
REVERT: A  493 LYS cc_start: 0.7882 (mmmm) cc_final: 0.7433 (ptpt)
REVERT: A  813 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7391 (pp20)
REVERT: A  879 GLU cc_start: 0.7146 (tt0) cc_final: 0.6461 (tp30)
REVERT: A  913 ARG cc_start: 0.4589 (OUTLIER) cc_final: 0.4185 (ptm160)
REVERT: A  922 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8781 (tttm)
REVERT: B   63 GLU cc_start: 0.8389 (mp0) cc_final: 0.8115 (mp0)
REVERT: B  358 GLU cc_start: 0.8508 (pm20) cc_final: 0.8012 (tt0)
REVERT: C   23 GLN cc_start: 0.7504 (mt0) cc_final: 0.7212 (mt0)
REVERT: C  272 LYS cc_start: 0.8023 (ptpp) cc_final: 0.7407 (mtpp)
REVERT: C  288 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7560 (tp-100)
  outliers start: 31
  outliers final: 13
  residues processed: 111
  average time/residue: 1.2346
  time to fit residues: 146.4664
Evaluate side-chains
  98 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  813 GLU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain A residue  922 LYS
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  350 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 58 optimal weight:    0.2980
   chunk 8 optimal weight:   20.0000
   chunk 93 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
A 648 GLN
B  58 HIS
C 288 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.163021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.117037 restraints weight = 10808.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.90
r_work: 0.3259 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3129
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3129 r_free = 0.3129    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3129
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.4444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8574  Z= 0.244
  Angle     :  0.527   6.912  11567  Z= 0.276
  Chirality :  0.040   0.156   1234
  Planarity :  0.004   0.032   1500
  Dihedral  :  4.567  37.826   1144
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 23.46 %
    Favored  : 72.92 %
  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:  1.11 (0.27), residues: 1016
  helix:  1.75 (0.22), residues: 563
  sheet:  0.28 (0.57), residues: 90
  loop : -0.74 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A 428 
 HIS   0.005   0.001   HIS C 348 
 PHE   0.016   0.001   PHE A 662 
 TYR   0.019   0.001   TYR A 740 
 ARG   0.007   0.001   ARG A 928 

*********************** 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
  116 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 83
  time to evaluate  : 0.944 
Fit side-chains
REVERT: A  342 SER cc_start: 0.3041 (OUTLIER) cc_final: 0.2499 (m)
REVERT: A  486 MET cc_start: 0.7574 (ptt) cc_final: 0.6992 (ptp)
REVERT: A  493 LYS cc_start: 0.7854 (mmmm) cc_final: 0.7406 (ptpt)
REVERT: A  530 ASN cc_start: 0.7492 (p0) cc_final: 0.7246 (p0)
REVERT: A  813 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7361 (pp20)
REVERT: A  879 GLU cc_start: 0.7171 (tt0) cc_final: 0.6570 (tp30)
REVERT: A  913 ARG cc_start: 0.4744 (OUTLIER) cc_final: 0.4337 (ptm160)
REVERT: B   63 GLU cc_start: 0.8356 (mp0) cc_final: 0.8061 (mp0)
REVERT: B   75 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8100 (tttt)
REVERT: B   93 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7970 (tp40)
REVERT: B  358 GLU cc_start: 0.8534 (pm20) cc_final: 0.8063 (tt0)
REVERT: C   23 GLN cc_start: 0.7608 (mt0) cc_final: 0.7303 (mt0)
REVERT: C  272 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7496 (mtpp)
  outliers start: 33
  outliers final: 16
  residues processed: 109
  average time/residue: 1.2728
  time to fit residues: 148.2516
Evaluate side-chains
  100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  533 THR
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  813 GLU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue  350 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 99 optimal weight:   10.0000
   chunk 100 optimal weight:    8.9990
   chunk 26 optimal weight:    0.5980
   chunk 98 optimal weight:    0.0370
   chunk 38 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7258

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

Flipped N/Q/H residues before XYZ refinement:
** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
B  58 HIS
** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.164504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.118613 restraints weight = 10820.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 1.81
r_work: 0.3285 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3153
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3153 r_free = 0.3153    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3153
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8574  Z= 0.167
  Angle     :  0.484   6.329  11567  Z= 0.253
  Chirality :  0.039   0.151   1234
  Planarity :  0.003   0.033   1500
  Dihedral  :  4.421  42.779   1144
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 24.34 %
    Favored  : 72.81 %
  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:  1.29 (0.27), residues: 1016
  helix:  1.87 (0.22), residues: 563
  sheet:  0.34 (0.58), residues: 90
  loop : -0.61 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 909 
 HIS   0.005   0.001   HIS C 348 
 PHE   0.014   0.001   PHE A 662 
 TYR   0.016   0.001   TYR B 304 
 ARG   0.004   0.000   ARG A 863 

*********************** 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
  109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 0.947 
Fit side-chains
REVERT: A  342 SER cc_start: 0.3053 (OUTLIER) cc_final: 0.2504 (m)
REVERT: A  486 MET cc_start: 0.7488 (ptt) cc_final: 0.6869 (ptp)
REVERT: A  493 LYS cc_start: 0.7861 (mmmm) cc_final: 0.7394 (ptpt)
REVERT: A  813 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7325 (pp20)
REVERT: A  879 GLU cc_start: 0.7280 (tt0) cc_final: 0.6582 (tp30)
REVERT: A  913 ARG cc_start: 0.4785 (OUTLIER) cc_final: 0.4398 (ptm160)
REVERT: A  924 MET cc_start: 0.8135 (ttm) cc_final: 0.7828 (ttt)
REVERT: B   63 GLU cc_start: 0.8338 (mp0) cc_final: 0.7988 (mp0)
REVERT: B   75 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7852 (tttt)
REVERT: B   93 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7893 (tp40)
REVERT: B  358 GLU cc_start: 0.8358 (pm20) cc_final: 0.7836 (tt0)
REVERT: C   23 GLN cc_start: 0.7465 (mt0) cc_final: 0.7226 (mt0)
REVERT: C  272 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7417 (mtpp)
REVERT: C  288 GLN cc_start: 0.7879 (tp40) cc_final: 0.7603 (tp-100)
  outliers start: 26
  outliers final: 13
  residues processed: 104
  average time/residue: 1.2788
  time to fit residues: 142.3825
Evaluate side-chains
  94 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  522 GLU
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  813 GLU
Chi-restraints excluded: chain A residue  815 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue  350 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 56 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 15 optimal weight:    0.3980
   chunk 86 optimal weight:    1.9990
   chunk 98 optimal weight:   10.0000
   chunk 6 optimal weight:    0.0770
   chunk 18 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
B  58 HIS
** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.165328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.125475 restraints weight = 10898.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.94
r_work: 0.3286 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3144
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3144 r_free = 0.3144    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3144
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.4738

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8574  Z= 0.143
  Angle     :  0.466   6.195  11567  Z= 0.245
  Chirality :  0.038   0.149   1234
  Planarity :  0.003   0.039   1500
  Dihedral  :  4.343  45.318   1144
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 24.34 %
    Favored  : 72.81 %
  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:  1.97 (0.22), residues: 563
  sheet:  0.47 (0.64), residues: 80
  loop : -0.54 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 136 
 HIS   0.004   0.001   HIS C 348 
 PHE   0.013   0.001   PHE A 662 
 TYR   0.020   0.001   TYR A 740 
 ARG   0.004   0.000   ARG A 402 

*********************** 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
  109 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 SER cc_start: 0.2930 (OUTLIER) cc_final: 0.2352 (m)
REVERT: A  486 MET cc_start: 0.7456 (ptt) cc_final: 0.6836 (ptp)
REVERT: A  493 LYS cc_start: 0.7902 (mmmm) cc_final: 0.7458 (ptpt)
REVERT: A  813 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7336 (pp20)
REVERT: A  879 GLU cc_start: 0.7295 (tt0) cc_final: 0.6598 (tp30)
REVERT: A  913 ARG cc_start: 0.4890 (OUTLIER) cc_final: 0.4521 (ptm160)
REVERT: A  924 MET cc_start: 0.8160 (ttm) cc_final: 0.7855 (ttt)
REVERT: B   63 GLU cc_start: 0.8432 (mp0) cc_final: 0.8103 (mp0)
REVERT: B   75 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7900 (tttt)
REVERT: B   93 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7864 (tp40)
REVERT: B  358 GLU cc_start: 0.8362 (pm20) cc_final: 0.7819 (tt0)
REVERT: C   23 GLN cc_start: 0.7294 (mt0) cc_final: 0.7057 (mt0)
REVERT: C  272 LYS cc_start: 0.7869 (ptpp) cc_final: 0.7411 (mtpp)
REVERT: C  288 GLN cc_start: 0.7917 (tp40) cc_final: 0.7679 (tp-100)
  outliers start: 26
  outliers final: 15
  residues processed: 105
  average time/residue: 1.2854
  time to fit residues: 144.2669
Evaluate side-chains
  99 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.892 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  813 GLU
Chi-restraints excluded: chain A residue  815 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  900 ARG
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue  350 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0980
   chunk 5 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
B  58 HIS
C 288 GLN
** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.162298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.116229 restraints weight = 10931.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.81
r_work: 0.3247 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3105
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3105 r_free = 0.3105    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3105
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.4962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8574  Z= 0.237
  Angle     :  0.520   7.039  11567  Z= 0.270
  Chirality :  0.040   0.156   1234
  Planarity :  0.003   0.037   1500
  Dihedral  :  4.652  53.132   1144
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 23.79 %
    Favored  : 72.81 %
  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:  1.26 (0.27), residues: 1016
  helix:  1.84 (0.22), residues: 563
  sheet:  0.43 (0.59), residues: 85
  loop : -0.63 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 313 
 HIS   0.005   0.001   HIS C 348 
 PHE   0.014   0.001   PHE A 662 
 TYR   0.018   0.001   TYR B 304 
 ARG   0.006   0.000   ARG B  37 

*********************** 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
  114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 83
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 SER cc_start: 0.2748 (OUTLIER) cc_final: 0.2173 (m)
REVERT: A  486 MET cc_start: 0.7293 (ptt) cc_final: 0.6579 (ptp)
REVERT: A  493 LYS cc_start: 0.7872 (mmmm) cc_final: 0.7426 (ptpt)
REVERT: A  813 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7365 (pp20)
REVERT: A  879 GLU cc_start: 0.7236 (tt0) cc_final: 0.6603 (tp30)
REVERT: A  913 ARG cc_start: 0.4970 (OUTLIER) cc_final: 0.4635 (ptm160)
REVERT: A  924 MET cc_start: 0.8222 (ttm) cc_final: 0.7794 (ttt)
REVERT: B   63 GLU cc_start: 0.8324 (mp0) cc_final: 0.7954 (mp0)
REVERT: B   75 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.7946 (tttt)
REVERT: B   93 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7850 (tp40)
REVERT: B  358 GLU cc_start: 0.8403 (pm20) cc_final: 0.7916 (tt0)
REVERT: C   23 GLN cc_start: 0.7426 (mt0) cc_final: 0.7174 (mt0)
REVERT: C  272 LYS cc_start: 0.7952 (ptpp) cc_final: 0.7491 (mtpp)
REVERT: C  288 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7820 (tp-100)
  outliers start: 31
  outliers final: 15
  residues processed: 108
  average time/residue: 1.3328
  time to fit residues: 153.1866
Evaluate side-chains
  99 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  626 ASP
Chi-restraints excluded: chain A residue  813 GLU
Chi-restraints excluded: chain A residue  815 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  900 ARG
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  350 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 40 optimal weight:    0.0470
   chunk 64 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 98 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    1.0480

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

Flipped N/Q/H residues before XYZ refinement:
B  58 HIS
C 288 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.162318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.116036 restraints weight = 10834.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.94
r_work: 0.3263 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3117
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3117 r_free = 0.3117    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3117
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.5050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8574  Z= 0.212
  Angle     :  0.506   6.788  11567  Z= 0.264
  Chirality :  0.040   0.143   1234
  Planarity :  0.003   0.037   1500
  Dihedral  :  4.650  57.139   1144
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 24.89 %
    Favored  : 72.37 %
  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:  1.26 (0.27), residues: 1016
  helix:  1.86 (0.22), residues: 563
  sheet:  0.36 (0.59), residues: 85
  loop : -0.63 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 313 
 HIS   0.004   0.001   HIS C 348 
 PHE   0.013   0.001   PHE A 662 
 TYR   0.019   0.001   TYR A 740 
 ARG   0.004   0.000   ARG B  37 

*********************** 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
  106 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 81
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 SER cc_start: 0.2678 (OUTLIER) cc_final: 0.2143 (m)
REVERT: A  486 MET cc_start: 0.7304 (ptt) cc_final: 0.6598 (ptp)
REVERT: A  493 LYS cc_start: 0.7872 (mmmm) cc_final: 0.7416 (ptpt)
REVERT: A  562 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6895 (mp0)
REVERT: A  813 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7340 (pp20)
REVERT: A  843 MET cc_start: 0.8935 (mtp) cc_final: 0.8533 (mtm)
REVERT: A  879 GLU cc_start: 0.7197 (tt0) cc_final: 0.6716 (tp30)
REVERT: A  913 ARG cc_start: 0.5114 (OUTLIER) cc_final: 0.4815 (ptm160)
REVERT: A  924 MET cc_start: 0.8369 (ttm) cc_final: 0.8050 (ttt)
REVERT: B   75 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8121 (tttt)
REVERT: B   93 GLN cc_start: 0.8227 (tm-30) cc_final: 0.8006 (tp40)
REVERT: B  358 GLU cc_start: 0.8505 (pm20) cc_final: 0.8106 (tt0)
REVERT: C   23 GLN cc_start: 0.7621 (mt0) cc_final: 0.7343 (mt0)
REVERT: C  272 LYS cc_start: 0.8062 (ptpp) cc_final: 0.7647 (mtpp)
REVERT: C  288 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7898 (tp-100)
REVERT: C  320 GLU cc_start: 0.5692 (OUTLIER) cc_final: 0.5190 (mm-30)
  outliers start: 25
  outliers final: 15
  residues processed: 101
  average time/residue: 1.3270
  time to fit residues: 142.9506
Evaluate side-chains
  100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  626 ASP
Chi-restraints excluded: chain A residue  813 GLU
Chi-restraints excluded: chain A residue  815 TYR
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  900 ARG
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue   86 SER
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue  288 GLN
Chi-restraints excluded: chain C residue  320 GLU
Chi-restraints excluded: chain C residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0570
   chunk 73 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0060
   chunk 82 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.4714

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

Flipped N/Q/H residues before XYZ refinement:
** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
B  58 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.163630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.117780 restraints weight = 10707.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 1.92
r_work: 0.3276 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3149 r_free = 0.3149    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.5089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8574  Z= 0.147
  Angle     :  0.476   6.391  11567  Z= 0.250
  Chirality :  0.038   0.145   1234
  Planarity :  0.003   0.037   1500
  Dihedral  :  4.584  59.681   1144
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 25.22 %
    Favored  : 72.48 %
  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:  1.41 (0.27), residues: 1016
  helix:  1.98 (0.22), residues: 563
  sheet:  0.42 (0.60), residues: 85
  loop : -0.58 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 313 
 HIS   0.004   0.001   HIS C 348 
 PHE   0.012   0.001   PHE A 662 
 TYR   0.017   0.001   TYR B 304 
 ARG   0.003   0.000   ARG A 402 

********************** 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
  101 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
REVERT: A  486 MET cc_start: 0.7268 (ptt) cc_final: 0.6873 (ptp)
REVERT: A  562 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6821 (mp0)
REVERT: A  743 PHE cc_start: 0.8422 (t80) cc_final: 0.8215 (t80)
REVERT: A  813 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7341 (pp20)
REVERT: A  854 MET cc_start: 0.8592 (mmt) cc_final: 0.8325 (mtt)
REVERT: A  879 GLU cc_start: 0.7152 (tt0) cc_final: 0.6694 (tp30)
REVERT: A  913 ARG cc_start: 0.5222 (OUTLIER) cc_final: 0.4925 (ptm160)
REVERT: A  924 MET cc_start: 0.8341 (ttm) cc_final: 0.8040 (ttt)
REVERT: B   75 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8151 (tttt)
REVERT: B  358 GLU cc_start: 0.8504 (pm20) cc_final: 0.8133 (tt0)
REVERT: C   23 GLN cc_start: 0.7591 (mt0) cc_final: 0.7322 (mt0)
REVERT: C  272 LYS cc_start: 0.8055 (ptpp) cc_final: 0.7693 (mtpp)
REVERT: C  288 GLN cc_start: 0.8285 (tp40) cc_final: 0.8031 (tp-100)
REVERT: C  320 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5478 (mm-30)
  outliers start: 21
  outliers final: 12
  residues processed: 97
  average time/residue: 1.2925
  time to fit residues: 133.7687
Evaluate side-chains
  91 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.996 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  562 GLU
Chi-restraints excluded: chain A residue  621 ILE
Chi-restraints excluded: chain A residue  626 ASP
Chi-restraints excluded: chain A residue  813 GLU
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  880 LEU
Chi-restraints excluded: chain A residue  913 ARG
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain B residue   12 VAL
Chi-restraints excluded: chain B residue   61 THR
Chi-restraints excluded: chain B residue   75 LYS
Chi-restraints excluded: chain B residue  103 VAL
Chi-restraints excluded: chain B residue  107 LEU
Chi-restraints excluded: chain B residue  225 VAL
Chi-restraints excluded: chain B residue  306 ILE
Chi-restraints excluded: chain C residue  320 GLU
Chi-restraints excluded: chain C residue  350 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0670
   chunk 12 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.7522

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

Flipped N/Q/H residues before XYZ refinement:
** A 603 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 656 HIS
B  58 HIS
C 288 GLN
** C 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.163116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.117305 restraints weight = 10805.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.3399 rms_B_bonded: 1.93
r_work: 0.3277 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3130
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3130 r_free = 0.3130    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3130
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.5204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8574  Z= 0.175
  Angle     :  0.492   6.541  11567  Z= 0.257
  Chirality :  0.039   0.149   1234
  Planarity :  0.003   0.036   1500
  Dihedral  :  4.571  58.397   1144
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 25.00 %
    Favored  : 72.59 %
  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:  1.40 (0.27), residues: 1016
  helix:  1.97 (0.22), residues: 563
  sheet:  0.39 (0.59), residues: 85
  loop : -0.56 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 909 
 HIS   0.003   0.001   HIS C 348 
 PHE   0.012   0.001   PHE A 662 
 TYR   0.020   0.001   TYR A 740 
 ARG   0.003   0.000   ARG B  37 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7086.35 seconds
wall clock time: 125 minutes 31.67 seconds (7531.67 seconds total)