Starting phenix.real_space_refine
on Sat Jun  7 04:01:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bpc_16149/06_2025/8bpc_16149_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bpc_16149/06_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_16149/06_2025/8bpc_16149.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bpc_16149/06_2025/8bpc_16149.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bpc_16149/06_2025/8bpc_16149_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bpc_16149/06_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-5710/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: 5.19, per 1000 atoms: 0.62
  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: 2.21
  Conformation dependent library (CDL) restraints added in 939.9 milliseconds
  
  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: 0.80
  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: 2.24

  Time building geometry restraints manager: 2.59 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:             0.690
  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:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.390
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.060
-------------------------------------------------------------------------------
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   8583  Z= 0.240
  Angle     :  0.687  10.650  11573  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13582 (  428)
  hydrogen bonds       : angle       5.87599 ( 1239)
  metal coordination   : bond        0.01223 (    9)
  metal coordination   : angle       1.78147 (    6)
  covalent geometry    : bond        0.00419 ( 8574)
  covalent geometry    : angle       0.68557 (11567)

*********************** 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  : 0.921 
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: 1.3680
  time to fit residues: 303.2422
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  : 0.995 
-------------------------------------------------------------------------------
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 = 45)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.118584 restraints weight = 10707.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 1.94
r_work: 0.3279 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3157
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    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 = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
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   8583  Z= 0.219
  Angle     :  0.654  12.317  11573  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05232 (  428)
  hydrogen bonds       : angle       4.42703 ( 1239)
  metal coordination   : bond        0.00944 (    9)
  metal coordination   : angle       2.34682 (    6)
  covalent geometry    : bond        0.00513 ( 8574)
  covalent geometry    : angle       0.65165 (11567)

*********************** 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  : 0.990 
Fit side-chains
REVERT: A  342 SER cc_start: 0.3622 (OUTLIER) cc_final: 0.3098 (m)
REVERT: A  395 LYS cc_start: 0.3768 (mttt) cc_final: 0.3085 (ttmt)
REVERT: A  476 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8488 (mp)
REVERT: A  486 MET cc_start: 0.7502 (ptt) cc_final: 0.6765 (ptp)
REVERT: A  493 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7454 (ptpt)
REVERT: A  631 GLU cc_start: 0.7725 (pt0) cc_final: 0.7225 (tp30)
REVERT: A  743 PHE cc_start: 0.8081 (t80) cc_final: 0.7768 (t80)
REVERT: A  813 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7436 (pt0)
REVERT: A  868 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7563 (mp)
REVERT: A  875 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7016 (mt)
REVERT: A  876 LYS cc_start: 0.7321 (tttt) cc_final: 0.6933 (tttt)
REVERT: A  913 ARG cc_start: 0.4334 (OUTLIER) cc_final: 0.3929 (ptm160)
REVERT: B   44 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8389 (mp)
REVERT: B   63 GLU cc_start: 0.8442 (mp0) cc_final: 0.8177 (mp0)
REVERT: B   75 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8072 (tttt)
REVERT: B  128 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.8175 (mt0)
REVERT: B  358 GLU cc_start: 0.8420 (pm20) cc_final: 0.8009 (tt0)
  outliers start: 59
  outliers final: 15
  residues processed: 152
  average time/residue: 1.4715
  time to fit residues: 236.1108
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  : 0.991 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 54 optimal weight:    0.1980
   chunk 72 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.167705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.121862 restraints weight = 10904.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.91
r_work: 0.3323 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3199
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3199 r_free = 0.3199    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 = 0.3199 r_free = 0.3199    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3199
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8583  Z= 0.121
  Angle     :  0.503   7.238  11573  Z= 0.267
  Chirality :  0.039   0.177   1234
  Planarity :  0.004   0.039   1500
  Dihedral  :  4.481  32.329   1144
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  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:  0.92 (0.64), residues: 74
  loop : -0.75 (0.31), residues: 381

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   0.013   0.001   PHE A 662 
 TYR   0.021   0.001   TYR A 740 
 ARG   0.006   0.000   ARG A 402 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04310 (  428)
  hydrogen bonds       : angle       4.16864 ( 1239)
  metal coordination   : bond        0.01198 (    9)
  metal coordination   : angle       1.42997 (    6)
  covalent geometry    : bond        0.00266 ( 8574)
  covalent geometry    : angle       0.50188 (11567)

*********************** 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
  130 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 95
  time to evaluate  : 0.949 
Fit side-chains
REVERT: A  342 SER cc_start: 0.3185 (OUTLIER) cc_final: 0.2618 (m)
REVERT: A  347 LEU cc_start: 0.6157 (mt) cc_final: 0.5900 (tt)
REVERT: A  456 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7863 (tt0)
REVERT: A  486 MET cc_start: 0.7410 (ptt) cc_final: 0.6836 (ptp)
REVERT: A  493 LYS cc_start: 0.7846 (mmmm) cc_final: 0.7423 (ptpt)
REVERT: A  530 ASN cc_start: 0.7613 (p0) cc_final: 0.7370 (p0)
REVERT: A  813 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7246 (pp20)
REVERT: A  913 ARG cc_start: 0.4630 (OUTLIER) cc_final: 0.4286 (ptm160)
REVERT: B   63 GLU cc_start: 0.8409 (mp0) cc_final: 0.8176 (mp0)
REVERT: B   75 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8264 (tttt)
REVERT: B  358 GLU cc_start: 0.8539 (pm20) cc_final: 0.8095 (tt0)
REVERT: C   23 GLN cc_start: 0.7530 (mt0) cc_final: 0.7244 (mt0)
REVERT: C  288 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7736 (tp-100)
  outliers start: 35
  outliers final: 12
  residues processed: 119
  average time/residue: 1.2429
  time to fit residues: 157.8643
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  : 0.947 
-------------------------------------------------------------------------------
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  456 GLU
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   48 LEU
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  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:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 68 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
A 756 HIS
B  40 HIS
B  58 HIS
C 288 GLN
C 321 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.164698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.118897 restraints weight = 10886.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.92
r_work: 0.3290 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3166 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    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 = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3158
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.4172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8583  Z= 0.130
  Angle     :  0.510   6.430  11573  Z= 0.267
  Chirality :  0.039   0.165   1234
  Planarity :  0.004   0.047   1500
  Dihedral  :  4.450  33.263   1144
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 23.36 %
    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:  1.19 (0.27), residues: 1016
  helix:  1.80 (0.22), residues: 563
  sheet:  0.75 (0.63), residues: 76
  loop : -0.75 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 434 
 HIS   0.005   0.001   HIS C 348 
 PHE   0.015   0.001   PHE A 662 
 TYR   0.017   0.001   TYR B 304 
 ARG   0.010   0.000   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04210 (  428)
  hydrogen bonds       : angle       4.07348 ( 1239)
  metal coordination   : bond        0.01208 (    9)
  metal coordination   : angle       2.14238 (    6)
  covalent geometry    : bond        0.00295 ( 8574)
  covalent geometry    : angle       0.50767 (11567)

*********************** 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: 30
    poor density    : 88
  time to evaluate  : 1.028 
Fit side-chains
REVERT: A  342 SER cc_start: 0.2995 (OUTLIER) cc_final: 0.2482 (m)
REVERT: A  444 LYS cc_start: 0.5015 (OUTLIER) cc_final: 0.4606 (pmmt)
REVERT: A  456 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7850 (tt0)
REVERT: A  486 MET cc_start: 0.7553 (ptt) cc_final: 0.6985 (ptp)
REVERT: A  493 LYS cc_start: 0.7855 (mmmm) cc_final: 0.7412 (ptpt)
REVERT: A  530 ASN cc_start: 0.7488 (p0) cc_final: 0.7253 (p0)
REVERT: A  813 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7393 (pp20)
REVERT: A  879 GLU cc_start: 0.7124 (tt0) cc_final: 0.6506 (tp30)
REVERT: A  913 ARG cc_start: 0.4604 (OUTLIER) cc_final: 0.4213 (ptm160)
REVERT: A  922 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8789 (tttm)
REVERT: B   63 GLU cc_start: 0.8378 (mp0) cc_final: 0.8079 (mp0)
REVERT: B   75 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8110 (tttt)
REVERT: B  358 GLU cc_start: 0.8517 (pm20) cc_final: 0.8012 (tt0)
REVERT: C   23 GLN cc_start: 0.7578 (mt0) cc_final: 0.7276 (mt0)
REVERT: C  272 LYS cc_start: 0.8049 (ptpp) cc_final: 0.7441 (mtpp)
REVERT: C  288 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7663 (tp-100)
  outliers start: 30
  outliers final: 14
  residues processed: 112
  average time/residue: 1.2122
  time to fit residues: 145.0296
Evaluate side-chains
  103 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 81
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
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  444 LYS
Chi-restraints excluded: chain A residue  456 GLU
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  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   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  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:    8.9990
   chunk 67 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 93 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 46 optimal weight:    0.4980
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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
B  93 GLN
C 288 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.162753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.115961 restraints weight = 10798.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.95
r_work: 0.3252 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3127 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3115
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3115 r_free = 0.3115    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 = 0.3115 r_free = 0.3115    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3115
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.4498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8583  Z= 0.155
  Angle     :  0.524   6.886  11573  Z= 0.273
  Chirality :  0.040   0.165   1234
  Planarity :  0.004   0.033   1500
  Dihedral  :  4.579  40.764   1144
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 23.14 %
    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:  1.14 (0.27), residues: 1016
  helix:  1.78 (0.22), residues: 563
  sheet:  0.23 (0.57), residues: 90
  loop : -0.72 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C 313 
 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   0.004   0.000   ARG A 863 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04371 (  428)
  hydrogen bonds       : angle       4.12226 ( 1239)
  metal coordination   : bond        0.01148 (    9)
  metal coordination   : angle       2.41130 (    6)
  covalent geometry    : bond        0.00363 ( 8574)
  covalent geometry    : angle       0.52133 (11567)

*********************** 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
  123 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 86
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A  342 SER cc_start: 0.3096 (OUTLIER) cc_final: 0.2546 (m)
REVERT: A  456 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7912 (tt0)
REVERT: A  486 MET cc_start: 0.7546 (ptt) cc_final: 0.6957 (ptp)
REVERT: A  493 LYS cc_start: 0.7831 (mmmm) cc_final: 0.7388 (ptpt)
REVERT: A  530 ASN cc_start: 0.7444 (p0) cc_final: 0.7228 (p0)
REVERT: A  813 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7365 (pp20)
REVERT: A  822 MET cc_start: 0.8733 (mtp) cc_final: 0.8466 (mtp)
REVERT: A  879 GLU cc_start: 0.7219 (tt0) cc_final: 0.6605 (tp30)
REVERT: A  913 ARG cc_start: 0.4748 (OUTLIER) cc_final: 0.4381 (ptm160)
REVERT: B   63 GLU cc_start: 0.8334 (mp0) cc_final: 0.8021 (mp0)
REVERT: B   75 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8051 (tttt)
REVERT: B  358 GLU cc_start: 0.8520 (pm20) cc_final: 0.8006 (tt0)
REVERT: C   23 GLN cc_start: 0.7582 (mt0) cc_final: 0.7280 (mt0)
REVERT: C  272 LYS cc_start: 0.7992 (ptpp) cc_final: 0.7491 (mtpp)
REVERT: C  288 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7645 (tp-100)
  outliers start: 37
  outliers final: 17
  residues processed: 114
  average time/residue: 1.2758
  time to fit residues: 155.1442
Evaluate side-chains
  104 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.927 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  456 GLU
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   44 LEU
Chi-restraints excluded: chain B residue   48 LEU
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  350 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 100 optimal weight:    4.9990
   chunk 26 optimal weight:    0.7980
   chunk 98 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 63 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B  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 = 0.3965 r_free = 0.3965 target = 0.163508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.117571 restraints weight = 10792.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3395 rms_B_bonded: 1.80
r_work: 0.3293 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3131
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3131 r_free = 0.3131    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 = 0.3131 r_free = 0.3131    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3131
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.4636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8583  Z= 0.129
  Angle     :  0.502   6.565  11573  Z= 0.262
  Chirality :  0.039   0.162   1234
  Planarity :  0.003   0.034   1500
  Dihedral  :  4.546  46.152   1144
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 23.57 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.27), residues: 1016
  helix:  1.83 (0.22), residues: 563
  sheet:  0.28 (0.58), residues: 90
  loop : -0.64 (0.31), 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   0.015   0.001   PHE A 662 
 TYR   0.017   0.001   TYR B 304 
 ARG   0.003   0.000   ARG A 900 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04088 (  428)
  hydrogen bonds       : angle       4.07651 ( 1239)
  metal coordination   : bond        0.01154 (    9)
  metal coordination   : angle       2.21572 (    6)
  covalent geometry    : bond        0.00295 ( 8574)
  covalent geometry    : angle       0.49945 (11567)

*********************** 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
  117 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 83
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: A  342 SER cc_start: 0.3099 (OUTLIER) cc_final: 0.2560 (m)
REVERT: A  347 LEU cc_start: 0.3983 (OUTLIER) cc_final: 0.3583 (mt)
REVERT: A  456 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7698 (tt0)
REVERT: A  486 MET cc_start: 0.7440 (ptt) cc_final: 0.6796 (ptp)
REVERT: A  493 LYS cc_start: 0.7894 (mmmm) cc_final: 0.7430 (ptpt)
REVERT: A  530 ASN cc_start: 0.7284 (p0) cc_final: 0.7078 (p0)
REVERT: A  813 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7327 (pp20)
REVERT: A  879 GLU cc_start: 0.7247 (tt0) cc_final: 0.6635 (tp30)
REVERT: A  913 ARG cc_start: 0.4765 (OUTLIER) cc_final: 0.4421 (ptm160)
REVERT: A  924 MET cc_start: 0.8188 (ttm) cc_final: 0.7863 (ttt)
REVERT: B   63 GLU cc_start: 0.8294 (mp0) cc_final: 0.7961 (mp0)
REVERT: B   75 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7859 (tttt)
REVERT: B  358 GLU cc_start: 0.8367 (pm20) cc_final: 0.7851 (tt0)
REVERT: C   23 GLN cc_start: 0.7486 (mt0) cc_final: 0.7240 (mt0)
REVERT: C  272 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7395 (mtpp)
REVERT: C  288 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7586 (tp-100)
  outliers start: 34
  outliers final: 19
  residues processed: 110
  average time/residue: 1.2889
  time to fit residues: 151.1157
Evaluate side-chains
  105 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  456 GLU
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  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   48 LEU
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  288 GLN
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:    0.6980
   chunk 33 optimal weight:    0.0020
   chunk 56 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0970
   chunk 86 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0980
   chunk 18 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   overall best weight:    0.3186

-------------------------------------------------------------------------------
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
B  93 GLN
C 288 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.165573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.119856 restraints weight = 10873.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 1.82
r_work: 0.3313 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    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 = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.4740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8583  Z= 0.097
  Angle     :  0.464   6.118  11573  Z= 0.244
  Chirality :  0.038   0.160   1234
  Planarity :  0.003   0.038   1500
  Dihedral  :  4.366  48.042   1144
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 24.12 %
    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:  1.42 (0.27), residues: 1016
  helix:  2.02 (0.22), residues: 563
  sheet:  0.28 (0.58), residues: 90
  loop : -0.59 (0.31), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 313 
 HIS   0.004   0.001   HIS C 348 
 PHE   0.012   0.001   PHE A 662 
 TYR   0.019   0.001   TYR A 740 
 ARG   0.004   0.000   ARG A 402 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (  428)
  hydrogen bonds       : angle       3.96127 ( 1239)
  metal coordination   : bond        0.01138 (    9)
  metal coordination   : angle       2.04457 (    6)
  covalent geometry    : bond        0.00201 ( 8574)
  covalent geometry    : angle       0.46152 (11567)

*********************** 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
  111 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 84
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 SER cc_start: 0.3075 (OUTLIER) cc_final: 0.2532 (m)
REVERT: A  347 LEU cc_start: 0.4056 (OUTLIER) cc_final: 0.3683 (mt)
REVERT: A  456 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7679 (tt0)
REVERT: A  486 MET cc_start: 0.7419 (ptt) cc_final: 0.6792 (ptp)
REVERT: A  493 LYS cc_start: 0.7902 (mmmm) cc_final: 0.7506 (ptpt)
REVERT: A  813 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7281 (pp20)
REVERT: A  879 GLU cc_start: 0.7281 (tt0) cc_final: 0.6633 (tp30)
REVERT: A  913 ARG cc_start: 0.4884 (OUTLIER) cc_final: 0.4528 (ptm160)
REVERT: A  924 MET cc_start: 0.8135 (ttm) cc_final: 0.7835 (ttt)
REVERT: B   63 GLU cc_start: 0.8344 (mp0) cc_final: 0.8011 (mp0)
REVERT: B   75 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7910 (tttt)
REVERT: B  358 GLU cc_start: 0.8326 (pm20) cc_final: 0.7816 (tt0)
REVERT: C   23 GLN cc_start: 0.7295 (mt0) cc_final: 0.7068 (mt0)
REVERT: C  272 LYS cc_start: 0.7897 (ptpp) cc_final: 0.7417 (mtpp)
REVERT: C  288 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.7516 (tp-100)
  outliers start: 27
  outliers final: 16
  residues processed: 106
  average time/residue: 1.1748
  time to fit residues: 133.2085
Evaluate side-chains
  102 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  456 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  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   48 LEU
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  288 GLN
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:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0570
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 93 optimal weight:    3.9990
   chunk 49 optimal weight:    9.9990
   chunk 8 optimal weight:    9.9990
   chunk 16 optimal weight:    3.9990
   chunk 66 optimal weight:    6.9990
   overall best weight:    1.0302

-------------------------------------------------------------------------------
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**
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 = 0.3965 r_free = 0.3965 target = 0.163428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.117535 restraints weight = 10931.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3391 rms_B_bonded: 1.81
r_work: 0.3289 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    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 = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.4843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8583  Z= 0.139
  Angle     :  0.498   6.675  11573  Z= 0.259
  Chirality :  0.039   0.161   1234
  Planarity :  0.003   0.037   1500
  Dihedral  :  4.571  52.367   1144
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 23.14 %
    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:  1.35 (0.27), residues: 1016
  helix:  1.94 (0.22), residues: 563
  sheet:  0.31 (0.58), residues: 90
  loop : -0.59 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 313 
 HIS   0.004   0.001   HIS C 348 
 PHE   0.014   0.001   PHE A 662 
 TYR   0.017   0.001   TYR B 304 
 ARG   0.005   0.000   ARG B  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04023 (  428)
  hydrogen bonds       : angle       4.00023 ( 1239)
  metal coordination   : bond        0.01515 (    9)
  metal coordination   : angle       2.08129 (    6)
  covalent geometry    : bond        0.00326 ( 8574)
  covalent geometry    : angle       0.49562 (11567)

*********************** 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
  115 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 SER cc_start: 0.2853 (OUTLIER) cc_final: 0.2305 (m)
REVERT: A  347 LEU cc_start: 0.4057 (OUTLIER) cc_final: 0.3667 (mt)
REVERT: A  456 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7732 (tt0)
REVERT: A  486 MET cc_start: 0.7328 (ptt) cc_final: 0.6633 (ptp)
REVERT: A  493 LYS cc_start: 0.7912 (mmmm) cc_final: 0.7494 (ptpt)
REVERT: A  813 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7329 (pp20)
REVERT: A  843 MET cc_start: 0.8658 (mtp) cc_final: 0.8305 (mtm)
REVERT: A  879 GLU cc_start: 0.7282 (tt0) cc_final: 0.6666 (tp30)
REVERT: A  913 ARG cc_start: 0.5023 (OUTLIER) cc_final: 0.4667 (ptm160)
REVERT: A  924 MET cc_start: 0.8197 (ttm) cc_final: 0.7869 (ttt)
REVERT: B   63 GLU cc_start: 0.8335 (mp0) cc_final: 0.7988 (mp0)
REVERT: B   75 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7889 (tttt)
REVERT: B  358 GLU cc_start: 0.8350 (pm20) cc_final: 0.7838 (tt0)
REVERT: C   23 GLN cc_start: 0.7397 (mt0) cc_final: 0.7141 (mt0)
REVERT: C  272 LYS cc_start: 0.7971 (ptpp) cc_final: 0.7509 (mtpp)
REVERT: C  288 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7224 (tm-30)
REVERT: C  320 GLU cc_start: 0.5329 (OUTLIER) cc_final: 0.4850 (mm-30)
  outliers start: 33
  outliers final: 17
  residues processed: 109
  average time/residue: 1.4444
  time to fit residues: 169.1817
Evaluate side-chains
  103 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  456 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  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   48 LEU
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  288 GLN
Chi-restraints excluded: chain C residue  320 GLU
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:    0.0370
   chunk 64 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 8 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 7 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 98 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0980
   overall best weight:    0.5058

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.164696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.118929 restraints weight = 10999.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.82
r_work: 0.3300 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    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 = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.4908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048   8583  Z= 0.104
  Angle     :  0.470   6.377  11573  Z= 0.246
  Chirality :  0.038   0.152   1234
  Planarity :  0.003   0.037   1500
  Dihedral  :  4.501  55.771   1144
  Min Nonbonded Distance : 2.003

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 24.01 %
    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:  1.46 (0.27), residues: 1016
  helix:  2.03 (0.22), residues: 563
  sheet:  0.41 (0.63), residues: 80
  loop : -0.54 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 313 
 HIS   0.004   0.001   HIS C 348 
 PHE   0.012   0.001   PHE A 662 
 TYR   0.019   0.001   TYR A 740 
 ARG   0.003   0.000   ARG B  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03703 (  428)
  hydrogen bonds       : angle       3.94149 ( 1239)
  metal coordination   : bond        0.01642 (    9)
  metal coordination   : angle       2.06318 (    6)
  covalent geometry    : bond        0.00226 ( 8574)
  covalent geometry    : angle       0.46748 (11567)

*********************** 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
  114 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 85
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: A  342 SER cc_start: 0.2700 (OUTLIER) cc_final: 0.2160 (m)
REVERT: A  347 LEU cc_start: 0.3902 (OUTLIER) cc_final: 0.3526 (mt)
REVERT: A  397 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7346 (tp)
REVERT: A  456 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7718 (tt0)
REVERT: A  486 MET cc_start: 0.7278 (ptt) cc_final: 0.6607 (ptp)
REVERT: A  493 LYS cc_start: 0.7881 (mmmm) cc_final: 0.7428 (ptpt)
REVERT: A  562 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6713 (mp0)
REVERT: A  813 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7330 (pp20)
REVERT: A  879 GLU cc_start: 0.7222 (tt0) cc_final: 0.6623 (tp30)
REVERT: A  913 ARG cc_start: 0.5150 (OUTLIER) cc_final: 0.4829 (ptm160)
REVERT: A  924 MET cc_start: 0.8141 (ttm) cc_final: 0.7825 (ttt)
REVERT: B   63 GLU cc_start: 0.8399 (mp0) cc_final: 0.8067 (mp0)
REVERT: B   75 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.7879 (tttt)
REVERT: B  358 GLU cc_start: 0.8346 (pm20) cc_final: 0.7826 (tt0)
REVERT: C  272 LYS cc_start: 0.7904 (ptpp) cc_final: 0.7476 (mtpp)
REVERT: C  288 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7131 (tm130)
REVERT: C  320 GLU cc_start: 0.5608 (OUTLIER) cc_final: 0.5035 (mm-30)
  outliers start: 29
  outliers final: 16
  residues processed: 107
  average time/residue: 1.8007
  time to fit residues: 207.2868
Evaluate side-chains
  104 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 1.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  456 GLU
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   48 LEU
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  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:    0.3980
   chunk 74 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 90 optimal weight:    0.0000
   chunk 82 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 60 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.7586

-------------------------------------------------------------------------------
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**
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 = 0.3971 r_free = 0.3971 target = 0.163776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.123300 restraints weight = 10813.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.03
r_work: 0.3254 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3114
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3114 r_free = 0.3114    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 = 0.3114 r_free = 0.3114    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3114
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.4989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8583  Z= 0.118
  Angle     :  0.488   6.530  11573  Z= 0.255
  Chirality :  0.039   0.153   1234
  Planarity :  0.003   0.036   1500
  Dihedral  :  4.554  59.046   1144
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 24.01 %
    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:  1.45 (0.27), residues: 1016
  helix:  2.01 (0.22), residues: 563
  sheet:  0.38 (0.62), residues: 80
  loop : -0.53 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 313 
 HIS   0.004   0.001   HIS C 348 
 PHE   0.012   0.001   PHE A 662 
 TYR   0.016   0.001   TYR B 304 
 ARG   0.004   0.000   ARG B  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03804 (  428)
  hydrogen bonds       : angle       3.95610 ( 1239)
  metal coordination   : bond        0.01524 (    9)
  metal coordination   : angle       2.23737 (    6)
  covalent geometry    : bond        0.00267 ( 8574)
  covalent geometry    : angle       0.48593 (11567)

********************** 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
  104 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 SER cc_start: 0.2663 (OUTLIER) cc_final: 0.2129 (m)
REVERT: A  347 LEU cc_start: 0.3922 (OUTLIER) cc_final: 0.3533 (mt)
REVERT: A  397 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7374 (tp)
REVERT: A  456 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7826 (tt0)
REVERT: A  486 MET cc_start: 0.7325 (ptt) cc_final: 0.6644 (ptp)
REVERT: A  493 LYS cc_start: 0.7876 (mmmm) cc_final: 0.7395 (ptpt)
REVERT: A  743 PHE cc_start: 0.8297 (t80) cc_final: 0.8077 (t80)
REVERT: A  813 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7373 (pp20)
REVERT: A  879 GLU cc_start: 0.7271 (tt0) cc_final: 0.6661 (tp30)
REVERT: A  913 ARG cc_start: 0.5231 (OUTLIER) cc_final: 0.4939 (ptm160)
REVERT: A  924 MET cc_start: 0.8194 (ttm) cc_final: 0.7876 (ttt)
REVERT: B   75 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7917 (tttt)
REVERT: B  358 GLU cc_start: 0.8400 (pm20) cc_final: 0.7857 (tt0)
REVERT: C   23 GLN cc_start: 0.7382 (mt0) cc_final: 0.7133 (mt0)
REVERT: C  272 LYS cc_start: 0.7984 (ptpp) cc_final: 0.7569 (mtpp)
REVERT: C  288 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7242 (tm130)
REVERT: C  320 GLU cc_start: 0.5656 (OUTLIER) cc_final: 0.5037 (mm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 97
  average time/residue: 1.2644
  time to fit residues: 131.0857
Evaluate side-chains
  100 residues out of total 923 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  342 SER
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  444 LYS
Chi-restraints excluded: chain A residue  456 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  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  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 36 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 81 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0870
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.9162

-------------------------------------------------------------------------------
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**
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 = 0.3964 r_free = 0.3964 target = 0.163134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.116601 restraints weight = 10888.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.89
r_work: 0.3260 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3163
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3163 r_free = 0.3163    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 = 0.3163 r_free = 0.3163    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3163
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.5084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8583  Z= 0.128
  Angle     :  0.496   6.539  11573  Z= 0.259
  Chirality :  0.039   0.151   1234
  Planarity :  0.003   0.035   1500
  Dihedral  :  4.585  59.153   1144
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 24.23 %
    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:  1.44 (0.27), residues: 1016
  helix:  2.00 (0.22), residues: 563
  sheet:  0.41 (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 C 313 
 HIS   0.004   0.001   HIS C 348 
 PHE   0.012   0.001   PHE A 662 
 TYR   0.018   0.001   TYR A 740 
 ARG   0.004   0.000   ARG B  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03908 (  428)
  hydrogen bonds       : angle       3.96716 ( 1239)
  metal coordination   : bond        0.01384 (    9)
  metal coordination   : angle       2.37550 (    6)
  covalent geometry    : bond        0.00294 ( 8574)
  covalent geometry    : angle       0.49285 (11567)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8340.10 seconds
wall clock time: 148 minutes 35.46 seconds (8915.46 seconds total)