Starting phenix.real_space_refine
on Wed Jun 11 17:49:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iv9_60922/06_2025/9iv9_60922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iv9_60922/06_2025/9iv9_60922.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.31
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iv9_60922/06_2025/9iv9_60922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iv9_60922/06_2025/9iv9_60922.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iv9_60922/06_2025/9iv9_60922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iv9_60922/06_2025/9iv9_60922.cif"
  }
  resolution = 2.31
  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=   0.056
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      84      5.16       5
     C    8293      2.51       5
     N    2239      2.21       5
     O    2430      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13048
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 10373
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1288, 10364
          Classifications: {'peptide': 1288}
          Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1239}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 1288, 10364
          Classifications: {'peptide': 1288}
          Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1239}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 10563
    Chain: "B"
      Number of atoms: 1215
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 151, 1212
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 5, 'TRANS': 145}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 151, 1212
          Classifications: {'peptide': 151}
          Link IDs: {'PTRANS': 5, 'TRANS': 145}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 1217
    Chain: "C"
      Number of atoms: 437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 437
          Classifications: {'peptide': 55}
          Link IDs: {'PTRANS': 2, 'TRANS': 52}
    Chain: "D"
      Number of atoms: 558
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 558
          Classifications: {'peptide': 71}
          Link IDs: {'PTRANS': 3, 'TRANS': 67}
    Chain: "E"
      Number of atoms: 463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 59, 463
          Classifications: {'peptide': 59}
          Link IDs: {'PTRANS': 2, 'TRANS': 56}
    Chain: "A"
      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}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8644  SG  CYS A1191      44.184  79.874 141.092  1.00118.99           S
  ATOM  10199  SG  CYS A1428      39.852  79.450 140.793  1.00148.85           S
  ATOM  10205  SG  CYS A1429      43.495  79.533 139.711  1.00134.84           S
  ATOM   8994  SG  CYS A1236      24.562  79.412 133.457  1.00106.68           S
  ATOM   9017  SG  CYS A1239      24.860  82.696 131.547  1.00100.45           S

  Time building chain proxies: 12.91, per 1000 atoms: 0.99
  Number of scatterers: 13048
  At special positions: 0
  Unit cell: (94.4438, 109.842, 168.356, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      84     16.00
     O    2430      8.00
     N    2239      7.00
     C    8293      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: 2.99
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1501 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A1191 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A1428 "
        pdb="ZN    ZN A1501 " - pdb=" SG  CYS A1429 "
      pdb="  ZN A1502 "
        pdb="ZN    ZN A1502 " - pdb=" NE2 HIS A1423 "
        pdb="ZN    ZN A1502 " - pdb=" ND1 HIS A1421 "
        pdb="ZN    ZN A1502 " - pdb=" SG  CYS A1239 "
        pdb="ZN    ZN A1502 " - pdb=" SG  CYS A1236 "
      Number of angles added : 1


  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3110

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 8 sheets defined
      60.7% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 33
      removed outlier: 3.810A  pdb=" N   LEU A  26 " --> pdb=" O   VAL A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 57
      removed outlier: 3.710A  pdb=" N   SER A  47 " --> pdb=" O   ASP A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 77
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 91 through 96
    Processing helix  chain 'A' and resid 104 through 137
      removed outlier: 3.731A  pdb=" N   ILE A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   LYS A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   LYS A 124 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 156
      removed outlier: 3.531A  pdb=" N   ASP A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 163
    Processing helix  chain 'A' and resid 166 through 189
    Processing helix  chain 'A' and resid 231 through 255
    Processing helix  chain 'A' and resid 260 through 273
      removed outlier: 3.723A  pdb=" N   ARG A 264 " --> pdb=" O   PRO A 260 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ASN A 266 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 282 through 288
      removed outlier: 4.002A  pdb=" N   ILE A 286 " --> pdb=" O   ARG A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 309 through 326
      removed outlier: 3.875A  pdb=" N   HIS A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 346
    Processing helix  chain 'A' and resid 349 through 355
    Processing helix  chain 'A' and resid 356 through 359
      removed outlier: 3.790A  pdb=" N   PHE A 359 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 356 through 359'
    Processing helix  chain 'A' and resid 369 through 382
      removed outlier: 3.551A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   HIS A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 409
    Processing helix  chain 'A' and resid 425 through 433
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 447 through 451
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 3.582A  pdb=" N   TRP A 483 " --> pdb=" O   LYS A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
    Processing helix  chain 'A' and resid 505 through 511
      removed outlier: 3.511A  pdb=" N   ASN A 511 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 526
      removed outlier: 3.725A  pdb=" N   VAL A 524 " --> pdb=" O   MET A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 574
    Processing helix  chain 'A' and resid 575 through 580
      removed outlier: 3.556A  pdb=" N   LYS A 580 " --> pdb=" O   LYS A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 595
    Processing helix  chain 'A' and resid 725 through 730
      removed outlier: 3.616A  pdb=" N   ASN A 729 " --> pdb=" O   LYS A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 747
      removed outlier: 5.018A  pdb=" N   ILE A 737 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 5.767A  pdb=" N   PHE A 738 " --> pdb=" O   SER A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 760
      removed outlier: 3.843A  pdb=" N   LYS A 757 " --> pdb=" O   ASN A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 784
      removed outlier: 3.656A  pdb=" N   THR A 784 " --> pdb=" O   LEU A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 822
      Proline residue:  A 812  - end of helix
    Processing helix  chain 'A' and resid 847 through 873
      removed outlier: 3.561A  pdb=" N   LEU A 873 " --> pdb=" O   ASN A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 911
      removed outlier: 4.045A  pdb=" N   SER A 908 " --> pdb=" O   GLN A 904 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ARG A 911 " --> pdb=" O   LYS A 907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 940
    Processing helix  chain 'A' and resid 943 through 965
    Processing helix  chain 'A' and resid 972 through 981
      Proline residue:  A 978  - end of helix
    Processing helix  chain 'A' and resid 982 through 992
    Processing helix  chain 'A' and resid 993 through 997
    Processing helix  chain 'A' and resid 1014 through 1029
    Processing helix  chain 'A' and resid 1033 through 1042
      removed outlier: 3.944A  pdb=" N   LEU A1037 " --> pdb=" O   THR A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1056
    Processing helix  chain 'A' and resid 1067 through 1077
    Processing helix  chain 'A' and resid 1086 through 1091
      removed outlier: 4.450A  pdb=" N   GLY A1091 " --> pdb=" O   PRO A1087 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1097 through 1110
    Processing helix  chain 'A' and resid 1115 through 1126
      removed outlier: 3.537A  pdb=" N   ASN A1125 " --> pdb=" O   GLU A1121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1138
      removed outlier: 3.520A  pdb=" N   LEU A1138 " --> pdb=" O   ILE A1134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1179
      removed outlier: 5.649A  pdb=" N   ASP A1166 " --> pdb=" O   LEU A1162 " (cutoff:3.500A)
      removed outlier: 5.532A  pdb=" N   TYR A1167 " --> pdb=" O   SER A1163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1191 through 1204
    Processing helix  chain 'A' and resid 1204 through 1209
    Processing helix  chain 'A' and resid 1236 through 1242
      removed outlier: 3.619A  pdb=" N   GLY A1242 " --> pdb=" O   ILE A1238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1291 through 1309
    Processing helix  chain 'A' and resid 1311 through 1323
    Processing helix  chain 'A' and resid 1329 through 1337
      removed outlier: 3.517A  pdb=" N   LEU A1333 " --> pdb=" O   ASP A1329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1374 through 1378
      removed outlier: 3.684A  pdb=" N   ASP A1378 " --> pdb=" O   ASP A1375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1391 through 1407
    Processing helix  chain 'B' and resid 526 through 574
      Proline residue:  B 544  - end of helix
    Processing helix  chain 'B' and resid 602 through 609
      removed outlier: 3.642A  pdb=" N   PHE B 609 " --> pdb=" O   GLN B 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 659 through 672
    Processing helix  chain 'B' and resid 674 through 687
    Processing helix  chain 'B' and resid 690 through 707
      removed outlier: 3.717A  pdb=" N   ILE B 694 " --> pdb=" O   ASN B 690 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 526 through 574
      Proline residue:  C 544  - end of helix
    Processing helix  chain 'D' and resid 526 through 578
      Proline residue:  D 544  - end of helix
    Processing helix  chain 'E' and resid 526 through 573
      Proline residue:  E 544  - end of helix
      removed outlier: 3.765A  pdb=" N   SER E 573 " --> pdb=" O   GLY E 569 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
    Processing sheet with id=AA2, first strand: chain 'A' and resid 385 through 388
    Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419
      removed outlier: 3.578A  pdb=" N   GLN A 454 " --> pdb=" O   TYR A 419 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 475 through 476
      removed outlier: 4.475A  pdb=" N   ARG A 503 " --> pdb=" O   LEU A 476 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 553 through 556
      removed outlier: 5.300A  pdb=" N   VAL A 537 " --> pdb=" O   VAL A 763 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR A 765 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 824 through 827
      removed outlier: 3.600A  pdb=" N   ARG A 824 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 888 through 891
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1225 through 1230

    747 hydrogen bonds defined for protein.
    2150 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: 4.73

  Time building geometry restraints manager: 3.61 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4099
        1.34 -     1.46: 1632
        1.46 -     1.57: 7406
        1.57 -     1.69: 1
        1.69 -     1.81: 140
  Bond restraints: 13278
  Sorted by residual:
  bond pdb=" C   ASN A 211 "
       pdb=" N   PRO A 212 "
    ideal  model  delta    sigma   weight residual
    1.337  1.375 -0.038 9.80e-03 1.04e+04 1.50e+01
  bond pdb=" CA  THR A 880 "
       pdb=" CB  THR A 880 "
    ideal  model  delta    sigma   weight residual
    1.531  1.606 -0.075 3.12e-02 1.03e+03 5.81e+00
  bond pdb=" CA  ILE B 543 "
       pdb=" C   ILE B 543 "
    ideal  model  delta    sigma   weight residual
    1.520  1.535 -0.015 8.80e-03 1.29e+04 2.88e+00
  bond pdb=" CA  GLY A1013 "
       pdb=" C   GLY A1013 "
    ideal  model  delta    sigma   weight residual
    1.530  1.513  0.017 1.04e-02 9.25e+03 2.78e+00
  bond pdb=" N   GLU C 542 "
       pdb=" CA  GLU C 542 "
    ideal  model  delta    sigma   weight residual
    1.459  1.478 -0.020 1.28e-02 6.10e+03 2.40e+00
  ... (remaining 13273 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 17588
        2.50 -     5.00: 284
        5.00 -     7.50: 37
        7.50 -    10.00: 9
       10.00 -    12.50: 2
  Bond angle restraints: 17920
  Sorted by residual:
  angle pdb=" C   ASP B 657 "
        pdb=" N   ASP B 658 "
        pdb=" CA  ASP B 658 "
      ideal   model   delta    sigma   weight residual
     121.54  130.30   -8.76 1.91e+00 2.74e-01 2.10e+01
  angle pdb=" C   ASP A 195 "
        pdb=" N   SER A 196 "
        pdb=" CA  SER A 196 "
      ideal   model   delta    sigma   weight residual
     121.54  129.81   -8.27 1.91e+00 2.74e-01 1.88e+01
  angle pdb=" N   GLU E 551 "
        pdb=" CA  GLU E 551 "
        pdb=" CB  GLU E 551 "
      ideal   model   delta    sigma   weight residual
     110.16  115.86   -5.70 1.48e+00 4.57e-01 1.48e+01
  angle pdb=" C   ASP D 530 "
        pdb=" N   MET D 531 "
        pdb=" CA  MET D 531 "
      ideal   model   delta    sigma   weight residual
     121.14  114.55    6.59 1.75e+00 3.27e-01 1.42e+01
  angle pdb=" C   ASN E 534 "
        pdb=" N   HIS E 535 "
        pdb=" CA  HIS E 535 "
      ideal   model   delta    sigma   weight residual
     121.14  114.81    6.33 1.75e+00 3.27e-01 1.31e+01
  ... (remaining 17915 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 7520
       17.33 -    34.65: 558
       34.65 -    51.98: 91
       51.98 -    69.31: 7
       69.31 -    86.63: 8
  Dihedral angle restraints: 8184
    sinusoidal: 3405
      harmonic: 4779
  Sorted by residual:
  dihedral pdb=" CA  ASN B 690 "
           pdb=" C   ASN B 690 "
           pdb=" N   ASP B 691 "
           pdb=" CA  ASP B 691 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.25  -22.75     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  ASN A 433 "
           pdb=" C   ASN A 433 "
           pdb=" N   SER A 434 "
           pdb=" CA  SER A 434 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.46   20.54     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  GLU A 388 "
           pdb=" C   GLU A 388 "
           pdb=" N   TYR A 389 "
           pdb=" CA  TYR A 389 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.72  -20.28     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 8181 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1549
       0.053 -    0.106: 376
       0.106 -    0.158: 108
       0.158 -    0.211: 12
       0.211 -    0.264: 4
  Chirality restraints: 2049
  Sorted by residual:
  chirality pdb=" CB  VAL C 540 "
            pdb=" CA  VAL C 540 "
            pdb=" CG1 VAL C 540 "
            pdb=" CG2 VAL C 540 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CB  VAL D 540 "
            pdb=" CA  VAL D 540 "
            pdb=" CG1 VAL D 540 "
            pdb=" CG2 VAL D 540 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CB  ILE C 536 "
            pdb=" CA  ILE C 536 "
            pdb=" CG1 ILE C 536 "
            pdb=" CG2 ILE C 536 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 2046 not shown)

  Planarity restraints: 2275
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 543 "    0.050 5.00e-02 4.00e+02   7.52e-02 9.04e+00
        pdb=" N   PRO C 544 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO C 544 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO C 544 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE E 543 "    0.037 5.00e-02 4.00e+02   5.57e-02 4.97e+00
        pdb=" N   PRO E 544 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO E 544 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO E 544 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  12 "    0.035 5.00e-02 4.00e+02   5.24e-02 4.40e+00
        pdb=" N   PRO A  13 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A  13 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A  13 "    0.029 5.00e-02 4.00e+02
  ... (remaining 2272 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 408
        2.73 -     3.27: 13321
        3.27 -     3.81: 21906
        3.81 -     4.36: 27248
        4.36 -     4.90: 45342
  Nonbonded interactions: 108225
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A1223 "
            pdb="ZN    ZN A1501 "
     model   vdw
     2.184 2.230
  nonbonded pdb=" N   ILE A 789 "
            pdb=" N   PHE A 790 "
     model   vdw
     2.561 2.560
  nonbonded pdb=" N   VAL A 491 "
            pdb=" N   LEU A 492 "
     model   vdw
     2.565 2.560
  nonbonded pdb=" N   ASN A 211 "
            pdb=" O   ASN A 211 "
     model   vdw
     2.566 2.496
  nonbonded pdb=" N   ASP A 203 "
            pdb=" O   ASP A 203 "
     model   vdw
     2.585 2.496
  ... (remaining 108220 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
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = (chain 'E' and resid 525 through 579)
}

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=0.48 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  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:          0.470
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     41.400
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.080
  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:             0.010
  Load rotamer database and sin/cos tables:14.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   58.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
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   0.075  13285  Z= 0.197
  Angle     :  0.799  12.496  17921  Z= 0.425
  Chirality :  0.051   0.264   2049
  Planarity :  0.006   0.077   2275
  Dihedral  : 12.337  86.632   5074
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.20), residues: 1604
  helix:  0.40 (0.16), residues: 901
  sheet:  0.58 (0.54), residues: 90
  loop : -0.41 (0.24), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1306 
 HIS   0.014   0.001   HIS E 535 
 PHE   0.020   0.002   PHE A 399 
 TYR   0.018   0.002   TYR A 389 
 ARG   0.010   0.001   ARG B 669 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11542 (  747)
  hydrogen bonds       : angle       5.70456 ( 2150)
  metal coordination   : bond        0.00453 (    7)
  metal coordination   : angle       4.34672 (    1)
  covalent geometry    : bond        0.00406 (13278)
  covalent geometry    : angle       0.79819 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  310 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 310
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LYS cc_start: 0.8966 (mmtp) cc_final: 0.8725 (mmmt)
REVERT: A  192 PHE cc_start: 0.8688 (m-80) cc_final: 0.8422 (m-80)
REVERT: A  460 GLU cc_start: 0.8112 (pm20) cc_final: 0.7792 (pm20)
REVERT: A  504 ARG cc_start: 0.8095 (mtm110) cc_final: 0.7842 (mtm-85)
REVERT: A  724 LYS cc_start: 0.8852 (mmpt) cc_final: 0.8610 (mmpt)
REVERT: A  788 ASP cc_start: 0.8148 (t70) cc_final: 0.7926 (t0)
REVERT: A  843 HIS cc_start: 0.8265 (t-90) cc_final: 0.7707 (t-90)
REVERT: A  907 LYS cc_start: 0.9375 (tttt) cc_final: 0.9144 (tttp)
REVERT: A 1124 ASP cc_start: 0.8703 (t70) cc_final: 0.8103 (t0)
REVERT: A 1155 GLN cc_start: 0.8663 (mp10) cc_final: 0.8308 (pm20)
REVERT: A 1225 MET cc_start: 0.8885 (mmt) cc_final: 0.8565 (mmt)
REVERT: A 1313 GLU cc_start: 0.8461 (tp30) cc_final: 0.8178 (mm-30)
REVERT: B  606 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8058 (mm-40)
REVERT: B  665 LYS cc_start: 0.8671 (tttm) cc_final: 0.8124 (tttm)
REVERT: B  699 ASN cc_start: 0.8864 (m110) cc_final: 0.8584 (m-40)
REVERT: C  550 LEU cc_start: 0.8920 (mt) cc_final: 0.8470 (tt)
REVERT: C  577 MET cc_start: 0.8422 (tmm) cc_final: 0.7888 (tmt)
REVERT: D  555 ARG cc_start: 0.8615 (mpp80) cc_final: 0.7905 (mpp80)
  outliers start: 0
  outliers final: 2
  residues processed: 310
  average time/residue: 1.4939
  time to fit residues: 498.0670
Evaluate side-chains
  246 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 244
  time to evaluate  : 1.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue 1426 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 135 optimal weight:    2.9990
   chunk 121 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 125 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 76 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0970
   chunk 145 optimal weight:    1.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
A 130 GLN
A 331 GLN
** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS
E 561 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.116506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.075810 restraints weight = 30127.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 3.48
r_work: 0.2759 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  13285  Z= 0.239
  Angle     :  0.663  11.807  17921  Z= 0.343
  Chirality :  0.046   0.159   2049
  Planarity :  0.005   0.060   2275
  Dihedral  :  5.332  86.195   1758
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.78 %
    Favored  : 86.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.15 (0.21), residues: 1604
  helix:  1.42 (0.17), residues: 907
  sheet:  0.26 (0.53), residues: 90
  loop : -0.05 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 173 
 HIS   0.009   0.001   HIS D 535 
 PHE   0.019   0.002   PHE A 726 
 TYR   0.017   0.002   TYR A 529 
 ARG   0.013   0.001   ARG B 675 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04988 (  747)
  hydrogen bonds       : angle       4.68980 ( 2150)
  metal coordination   : bond        0.00884 (    7)
  metal coordination   : angle       2.74472 (    1)
  covalent geometry    : bond        0.00556 (13278)
  covalent geometry    : angle       0.66254 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 249
  time to evaluate  : 1.790 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  192 PHE cc_start: 0.8495 (m-80) cc_final: 0.8105 (m-80)
REVERT: A  460 GLU cc_start: 0.8305 (pm20) cc_final: 0.8070 (pm20)
REVERT: A  724 LYS cc_start: 0.8876 (mmpt) cc_final: 0.8591 (mmpt)
REVERT: A  788 ASP cc_start: 0.8144 (t70) cc_final: 0.7757 (t0)
REVERT: A  843 HIS cc_start: 0.8047 (t-90) cc_final: 0.7845 (t-90)
REVERT: A 1099 ASP cc_start: 0.8969 (m-30) cc_final: 0.8734 (m-30)
REVERT: A 1121 GLU cc_start: 0.8872 (tt0) cc_final: 0.8584 (tt0)
REVERT: A 1124 ASP cc_start: 0.8881 (t70) cc_final: 0.8368 (t0)
REVERT: A 1225 MET cc_start: 0.8824 (mmt) cc_final: 0.8423 (mmt)
REVERT: A 1313 GLU cc_start: 0.8558 (tp30) cc_final: 0.8334 (mm-30)
REVERT: B  555 ARG cc_start: 0.9194 (mtm110) cc_final: 0.8911 (mtm110)
REVERT: B  606 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7948 (mm-40)
REVERT: B  665 LYS cc_start: 0.8512 (tttm) cc_final: 0.7973 (tttm)
REVERT: B  669 ARG cc_start: 0.8484 (mtt-85) cc_final: 0.8173 (mtt90)
REVERT: B  699 ASN cc_start: 0.8806 (m110) cc_final: 0.8563 (m-40)
REVERT: C  550 LEU cc_start: 0.8768 (mt) cc_final: 0.8369 (tt)
REVERT: C  577 MET cc_start: 0.8157 (tmm) cc_final: 0.7649 (tmt)
  outliers start: 22
  outliers final: 9
  residues processed: 256
  average time/residue: 1.4308
  time to fit residues: 396.6406
Evaluate side-chains
  238 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 229
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain A residue 1426 ASP
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain E residue  560 THR
Chi-restraints excluded: chain E residue  561 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 120 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 109 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   chunk 142 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 138 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A1066 GLN
** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.118373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.077489 restraints weight = 35707.523|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 3.76
r_work: 0.2785 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13285  Z= 0.134
  Angle     :  0.584   9.683  17921  Z= 0.300
  Chirality :  0.043   0.161   2049
  Planarity :  0.004   0.054   2275
  Dihedral  :  4.341  18.849   1756
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 13.21 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.57 (0.21), residues: 1604
  helix:  1.82 (0.18), residues: 908
  sheet:  0.27 (0.54), residues: 90
  loop :  0.05 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1306 
 HIS   0.008   0.001   HIS D 535 
 PHE   0.016   0.001   PHE A 399 
 TYR   0.013   0.001   TYR A 793 
 ARG   0.010   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04316 (  747)
  hydrogen bonds       : angle       4.47517 ( 2150)
  metal coordination   : bond        0.00427 (    7)
  metal coordination   : angle       3.76447 (    1)
  covalent geometry    : bond        0.00302 (13278)
  covalent geometry    : angle       0.58311 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 239
  time to evaluate  : 1.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LYS cc_start: 0.9022 (mmtp) cc_final: 0.8752 (mttt)
REVERT: A   81 LYS cc_start: 0.9251 (mtmm) cc_final: 0.9043 (mppt)
REVERT: A  192 PHE cc_start: 0.8478 (m-80) cc_final: 0.8055 (m-80)
REVERT: A  460 GLU cc_start: 0.8276 (pm20) cc_final: 0.7995 (pm20)
REVERT: A  467 LEU cc_start: 0.9348 (mm) cc_final: 0.9141 (tp)
REVERT: A  552 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7723 (mt)
REVERT: A  724 LYS cc_start: 0.8857 (mmpt) cc_final: 0.8564 (mmpt)
REVERT: A  788 ASP cc_start: 0.8104 (t70) cc_final: 0.7735 (t0)
REVERT: A 1066 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7962 (tm-30)
REVERT: A 1124 ASP cc_start: 0.8927 (t70) cc_final: 0.8447 (t0)
REVERT: A 1225 MET cc_start: 0.8934 (mmt) cc_final: 0.8514 (mmt)
REVERT: A 1313 GLU cc_start: 0.8553 (tp30) cc_final: 0.8312 (mm-30)
REVERT: B  554 ASP cc_start: 0.8599 (m-30) cc_final: 0.8275 (m-30)
REVERT: B  606 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7886 (mm-40)
REVERT: B  665 LYS cc_start: 0.8444 (tttm) cc_final: 0.7891 (tttm)
REVERT: B  669 ARG cc_start: 0.8390 (mtt-85) cc_final: 0.8055 (mtt90)
REVERT: B  699 ASN cc_start: 0.8758 (m110) cc_final: 0.8512 (m-40)
REVERT: C  550 LEU cc_start: 0.8832 (mt) cc_final: 0.8364 (tt)
REVERT: C  564 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7929 (tp)
REVERT: C  577 MET cc_start: 0.8135 (tmm) cc_final: 0.7389 (tmt)
REVERT: D  575 MET cc_start: 0.8533 (mtp) cc_final: 0.7732 (mtp)
REVERT: E  559 LYS cc_start: 0.9127 (tmmt) cc_final: 0.8891 (tmmt)
REVERT: E  561 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7843 (m-40)
  outliers start: 22
  outliers final: 8
  residues processed: 249
  average time/residue: 1.4647
  time to fit residues: 395.0305
Evaluate side-chains
  243 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 231
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue 1066 GLN
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain C residue  564 LEU
Chi-restraints excluded: chain C residue  573 SER
Chi-restraints excluded: chain E residue  561 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 129 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 94 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 101 optimal weight:    7.9990
   chunk 136 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 130 optimal weight:    0.5980
   chunk 21 optimal weight:    3.9990
   overall best weight:    2.0586

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.115588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.074394 restraints weight = 35760.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 3.77
r_work: 0.2721 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2720 r_free = 0.2720    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.058  13285  Z= 0.238
  Angle     :  0.637  11.707  17921  Z= 0.326
  Chirality :  0.045   0.153   2049
  Planarity :  0.004   0.051   2275
  Dihedral  :  4.462  20.911   1754
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.89 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.55 (0.21), residues: 1604
  helix:  1.83 (0.17), residues: 906
  sheet: -0.06 (0.52), residues: 90
  loop :  0.07 (0.25), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A1306 
 HIS   0.008   0.001   HIS E 535 
 PHE   0.024   0.002   PHE A 726 
 TYR   0.016   0.002   TYR A 529 
 ARG   0.011   0.001   ARG B 678 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04773 (  747)
  hydrogen bonds       : angle       4.55757 ( 2150)
  metal coordination   : bond        0.01182 (    7)
  metal coordination   : angle       1.57346 (    1)
  covalent geometry    : bond        0.00559 (13278)
  covalent geometry    : angle       0.63682 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 244
  time to evaluate  : 1.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 LYS cc_start: 0.9043 (mmtp) cc_final: 0.8685 (mmmt)
REVERT: A   81 LYS cc_start: 0.9251 (mtmm) cc_final: 0.9043 (mppt)
REVERT: A  192 PHE cc_start: 0.8474 (m-80) cc_final: 0.7968 (m-80)
REVERT: A  460 GLU cc_start: 0.8325 (pm20) cc_final: 0.8068 (pm20)
REVERT: A  534 GLN cc_start: 0.8853 (mt0) cc_final: 0.8166 (mm-40)
REVERT: A  724 LYS cc_start: 0.8890 (mmpt) cc_final: 0.8634 (mmpt)
REVERT: A  761 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8667 (mtm180)
REVERT: A  788 ASP cc_start: 0.8187 (t70) cc_final: 0.7802 (t0)
REVERT: A  834 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6998 (pm20)
REVERT: A  893 LYS cc_start: 0.9093 (mtpt) cc_final: 0.8874 (mtpp)
REVERT: A 1099 ASP cc_start: 0.8977 (m-30) cc_final: 0.8748 (m-30)
REVERT: A 1124 ASP cc_start: 0.8983 (t70) cc_final: 0.8534 (t0)
REVERT: A 1225 MET cc_start: 0.8932 (mmt) cc_final: 0.8499 (mmt)
REVERT: A 1313 GLU cc_start: 0.8551 (tp30) cc_final: 0.8309 (mm-30)
REVERT: A 1438 GLN cc_start: 0.8493 (tt0) cc_final: 0.8140 (tm-30)
REVERT: A 1442 GLU cc_start: 0.8224 (mp0) cc_final: 0.7883 (mp0)
REVERT: B  549 LYS cc_start: 0.8568 (tttm) cc_final: 0.8205 (tttt)
REVERT: B  554 ASP cc_start: 0.8655 (m-30) cc_final: 0.8335 (m-30)
REVERT: B  606 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7881 (mm-40)
REVERT: B  665 LYS cc_start: 0.8478 (tttm) cc_final: 0.8011 (tttm)
REVERT: B  669 ARG cc_start: 0.8351 (mtt-85) cc_final: 0.8141 (mmt90)
REVERT: B  699 ASN cc_start: 0.8731 (m110) cc_final: 0.8484 (m-40)
REVERT: C  550 LEU cc_start: 0.8783 (mt) cc_final: 0.8563 (mt)
REVERT: C  564 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7829 (tp)
REVERT: C  577 MET cc_start: 0.8187 (tmm) cc_final: 0.7750 (tmt)
REVERT: D  555 ARG cc_start: 0.8518 (mpp80) cc_final: 0.8217 (mpp80)
REVERT: E  581 LYS cc_start: 0.8708 (tppt) cc_final: 0.8354 (mppt)
  outliers start: 30
  outliers final: 15
  residues processed: 259
  average time/residue: 1.4775
  time to fit residues: 412.5820
Evaluate side-chains
  248 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 230
  time to evaluate  : 1.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 ILE
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  761 ARG
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  834 GLU
Chi-restraints excluded: chain A residue 1203 MET
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain C residue  564 LEU
Chi-restraints excluded: chain C residue  573 SER
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain E residue  551 GLU
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 55 optimal weight:    0.7980
   chunk 78 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 93 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 133 optimal weight:    3.9990
   chunk 151 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A 427 HIS
** A 843 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS
B 561 ASN
B 648 ASN
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.117367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.076526 restraints weight = 33988.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.2942 rms_B_bonded: 3.70
r_work: 0.2769 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2771
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2771 r_free = 0.2771    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2771 r_free = 0.2771    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2771
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13285  Z= 0.139
  Angle     :  0.608   9.227  17921  Z= 0.310
  Chirality :  0.042   0.157   2049
  Planarity :  0.004   0.049   2275
  Dihedral  :  4.298  21.938   1754
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.77 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.68 (0.21), residues: 1604
  helix:  1.94 (0.17), residues: 914
  sheet:  0.01 (0.53), residues: 90
  loop :  0.08 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A1306 
 HIS   0.008   0.001   HIS D 535 
 PHE   0.016   0.001   PHE A 399 
 TYR   0.011   0.001   TYR A 284 
 ARG   0.012   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04277 (  747)
  hydrogen bonds       : angle       4.42000 ( 2150)
  metal coordination   : bond        0.00381 (    7)
  metal coordination   : angle       3.28484 (    1)
  covalent geometry    : bond        0.00315 (13278)
  covalent geometry    : angle       0.60796 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 245
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.9234 (mtmm) cc_final: 0.9009 (mppt)
REVERT: A  192 PHE cc_start: 0.8470 (m-80) cc_final: 0.7963 (m-80)
REVERT: A  460 GLU cc_start: 0.8296 (pm20) cc_final: 0.8035 (pm20)
REVERT: A  552 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7762 (mt)
REVERT: A  724 LYS cc_start: 0.8867 (mmpt) cc_final: 0.8616 (mmpt)
REVERT: A  788 ASP cc_start: 0.8102 (t70) cc_final: 0.7711 (t0)
REVERT: A  834 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.7048 (pm20)
REVERT: A  893 LYS cc_start: 0.9139 (mtpt) cc_final: 0.8921 (mtpp)
REVERT: A 1124 ASP cc_start: 0.9001 (t70) cc_final: 0.8543 (t0)
REVERT: A 1225 MET cc_start: 0.8912 (mmt) cc_final: 0.8492 (mmt)
REVERT: A 1313 GLU cc_start: 0.8495 (tp30) cc_final: 0.8225 (mm-30)
REVERT: A 1442 GLU cc_start: 0.8167 (mp0) cc_final: 0.7823 (mp0)
REVERT: B  554 ASP cc_start: 0.8655 (m-30) cc_final: 0.8307 (m-30)
REVERT: B  606 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7874 (mm-40)
REVERT: B  665 LYS cc_start: 0.8379 (tttm) cc_final: 0.7823 (tttm)
REVERT: B  669 ARG cc_start: 0.8294 (mtt-85) cc_final: 0.8078 (mmt90)
REVERT: C  564 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7948 (tp)
REVERT: C  577 MET cc_start: 0.8195 (tmm) cc_final: 0.7504 (tmt)
REVERT: D  547 ILE cc_start: 0.8895 (mm) cc_final: 0.8636 (tp)
REVERT: E  581 LYS cc_start: 0.8659 (tppt) cc_final: 0.8359 (mppt)
  outliers start: 29
  outliers final: 17
  residues processed: 258
  average time/residue: 1.4187
  time to fit residues: 396.4099
Evaluate side-chains
  249 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 229
  time to evaluate  : 1.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  834 GLU
Chi-restraints excluded: chain A residue  922 GLU
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain C residue  564 LEU
Chi-restraints excluded: chain C residue  573 SER
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain D residue  560 THR
Chi-restraints excluded: chain E residue  551 GLU
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 107 optimal weight:    0.4980
   chunk 2 optimal weight:    0.5980
   chunk 147 optimal weight:    0.9990
   chunk 148 optimal weight:   40.0000
   chunk 21 optimal weight:    0.7980
   chunk 153 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 54 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 156 optimal weight:    9.9990
   chunk 136 optimal weight:    6.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A 427 HIS
A1066 GLN
** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS
B 648 ASN
D 561 ASN
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.117299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.076939 restraints weight = 29953.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 3.45
r_work: 0.2788 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2790
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2790 r_free = 0.2790    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2790
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13285  Z= 0.137
  Angle     :  0.597   9.692  17921  Z= 0.304
  Chirality :  0.042   0.167   2049
  Planarity :  0.004   0.054   2275
  Dihedral  :  4.246  21.860   1754
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 14.84 %
    Favored  : 82.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.76 (0.21), residues: 1604
  helix:  2.00 (0.17), residues: 915
  sheet:  0.02 (0.53), residues: 90
  loop :  0.13 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A1306 
 HIS   0.009   0.001   HIS E 535 
 PHE   0.017   0.001   PHE A 399 
 TYR   0.011   0.001   TYR A 284 
 ARG   0.012   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04185 (  747)
  hydrogen bonds       : angle       4.38333 ( 2150)
  metal coordination   : bond        0.00375 (    7)
  metal coordination   : angle       2.63426 (    1)
  covalent geometry    : bond        0.00311 (13278)
  covalent geometry    : angle       0.59644 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 240
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.9226 (mtmm) cc_final: 0.9010 (mppt)
REVERT: A  192 PHE cc_start: 0.8475 (m-80) cc_final: 0.7970 (m-80)
REVERT: A  193 ARG cc_start: 0.8431 (mmp80) cc_final: 0.8128 (mmp80)
REVERT: A  460 GLU cc_start: 0.8311 (pm20) cc_final: 0.8030 (pm20)
REVERT: A  552 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7817 (mt)
REVERT: A  724 LYS cc_start: 0.8883 (mmpt) cc_final: 0.8636 (mmpt)
REVERT: A  788 ASP cc_start: 0.8113 (t70) cc_final: 0.7733 (t0)
REVERT: A  834 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7038 (pm20)
REVERT: A  893 LYS cc_start: 0.9142 (mtpt) cc_final: 0.8922 (mtpp)
REVERT: A 1099 ASP cc_start: 0.8974 (m-30) cc_final: 0.8728 (m-30)
REVERT: A 1124 ASP cc_start: 0.8998 (t70) cc_final: 0.8571 (t0)
REVERT: A 1225 MET cc_start: 0.8898 (mmt) cc_final: 0.8472 (mmt)
REVERT: A 1313 GLU cc_start: 0.8492 (tp30) cc_final: 0.8219 (mm-30)
REVERT: A 1392 TYR cc_start: 0.6852 (m-80) cc_final: 0.6583 (m-80)
REVERT: A 1442 GLU cc_start: 0.8152 (mp0) cc_final: 0.7801 (mp0)
REVERT: B  554 ASP cc_start: 0.8636 (m-30) cc_final: 0.8297 (m-30)
REVERT: B  606 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7872 (mm-40)
REVERT: B  665 LYS cc_start: 0.8313 (tttm) cc_final: 0.7763 (tttm)
REVERT: B  669 ARG cc_start: 0.8340 (mtt-85) cc_final: 0.8041 (mmt90)
REVERT: B  695 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8089 (mp10)
REVERT: C  564 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7799 (tp)
REVERT: C  577 MET cc_start: 0.8246 (tmm) cc_final: 0.7561 (tmt)
REVERT: E  581 LYS cc_start: 0.8632 (tppt) cc_final: 0.8271 (mppt)
  outliers start: 35
  outliers final: 14
  residues processed: 253
  average time/residue: 1.5879
  time to fit residues: 438.6420
Evaluate side-chains
  250 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 232
  time to evaluate  : 1.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  834 GLU
Chi-restraints excluded: chain A residue 1203 MET
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain B residue  695 GLN
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain C residue  564 LEU
Chi-restraints excluded: chain C residue  573 SER
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain E residue  551 GLU
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 148 optimal weight:   40.0000
   chunk 25 optimal weight:    0.4980
   chunk 130 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 128 optimal weight:    6.9990
   chunk 131 optimal weight:    4.9990
   chunk 106 optimal weight:    0.4980
   chunk 83 optimal weight:    0.5980
   chunk 1 optimal weight:    5.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A 427 HIS
** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS
B 648 ASN
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.118026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.077063 restraints weight = 33672.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.68
r_work: 0.2789 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2791 r_free = 0.2791    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  13285  Z= 0.134
  Angle     :  0.618  12.522  17921  Z= 0.313
  Chirality :  0.042   0.221   2049
  Planarity :  0.004   0.055   2275
  Dihedral  :  4.226  22.188   1754
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.13 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.78 (0.21), residues: 1604
  helix:  2.00 (0.18), residues: 914
  sheet:  0.20 (0.51), residues: 97
  loop :  0.15 (0.26), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1306 
 HIS   0.009   0.001   HIS E 535 
 PHE   0.016   0.001   PHE A 399 
 TYR   0.011   0.001   TYR A 284 
 ARG   0.013   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04134 (  747)
  hydrogen bonds       : angle       4.36893 ( 2150)
  metal coordination   : bond        0.00332 (    7)
  metal coordination   : angle       2.59499 (    1)
  covalent geometry    : bond        0.00304 (13278)
  covalent geometry    : angle       0.61750 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 242
  time to evaluate  : 1.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8655 (t0) cc_final: 0.8254 (t0)
REVERT: A   81 LYS cc_start: 0.9229 (mtmm) cc_final: 0.9015 (mppt)
REVERT: A  192 PHE cc_start: 0.8462 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  193 ARG cc_start: 0.8438 (mmp80) cc_final: 0.8126 (mmp80)
REVERT: A  460 GLU cc_start: 0.8334 (pm20) cc_final: 0.8043 (pm20)
REVERT: A  724 LYS cc_start: 0.8885 (mmpt) cc_final: 0.8618 (mmpt)
REVERT: A  788 ASP cc_start: 0.8091 (t70) cc_final: 0.7696 (t0)
REVERT: A  824 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.7920 (ttm110)
REVERT: A  834 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7013 (pm20)
REVERT: A 1124 ASP cc_start: 0.8975 (t70) cc_final: 0.8582 (t0)
REVERT: A 1225 MET cc_start: 0.8908 (mmt) cc_final: 0.8484 (mmt)
REVERT: A 1313 GLU cc_start: 0.8485 (tp30) cc_final: 0.8208 (mm-30)
REVERT: A 1440 ASP cc_start: 0.8317 (m-30) cc_final: 0.7983 (m-30)
REVERT: A 1442 GLU cc_start: 0.8138 (mp0) cc_final: 0.7776 (mp0)
REVERT: B  554 ASP cc_start: 0.8589 (m-30) cc_final: 0.8248 (m-30)
REVERT: B  606 GLN cc_start: 0.8259 (mm-40) cc_final: 0.7852 (mm-40)
REVERT: B  665 LYS cc_start: 0.8292 (tttm) cc_final: 0.8071 (ttmm)
REVERT: B  669 ARG cc_start: 0.8377 (mtt-85) cc_final: 0.7986 (mmt90)
REVERT: C  564 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7937 (tp)
REVERT: C  577 MET cc_start: 0.8255 (tmm) cc_final: 0.7386 (tmt)
REVERT: D  555 ARG cc_start: 0.8494 (mtm-85) cc_final: 0.8293 (mtm-85)
REVERT: E  581 LYS cc_start: 0.8622 (tppt) cc_final: 0.8251 (mppt)
  outliers start: 23
  outliers final: 13
  residues processed: 252
  average time/residue: 1.5392
  time to fit residues: 422.6464
Evaluate side-chains
  253 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 238
  time to evaluate  : 1.668 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  834 GLU
Chi-restraints excluded: chain A residue  922 GLU
Chi-restraints excluded: chain A residue 1203 MET
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain C residue  564 LEU
Chi-restraints excluded: chain C residue  573 SER
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain E residue  551 GLU
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 132 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 152 optimal weight:    5.9990
   chunk 64 optimal weight:    4.9990
   chunk 28 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 150 optimal weight:    0.9980
   chunk 129 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A 427 HIS
** A1125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS
B 648 ASN
D 561 ASN
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 561 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.117378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.076482 restraints weight = 34138.538|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 3.69
r_work: 0.2779 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13285  Z= 0.145
  Angle     :  0.620  10.495  17921  Z= 0.314
  Chirality :  0.043   0.166   2049
  Planarity :  0.004   0.059   2275
  Dihedral  :  4.204  22.035   1754
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.07 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.78 (0.21), residues: 1604
  helix:  1.99 (0.18), residues: 916
  sheet:  0.11 (0.54), residues: 90
  loop :  0.16 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1306 
 HIS   0.009   0.001   HIS E 535 
 PHE   0.017   0.001   PHE A 399 
 TYR   0.013   0.001   TYR A 284 
 ARG   0.014   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  747)
  hydrogen bonds       : angle       4.39271 ( 2150)
  metal coordination   : bond        0.00413 (    7)
  metal coordination   : angle       2.27678 (    1)
  covalent geometry    : bond        0.00334 (13278)
  covalent geometry    : angle       0.61968 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 242
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.9227 (mtmm) cc_final: 0.9011 (mppt)
REVERT: A  192 PHE cc_start: 0.8461 (m-80) cc_final: 0.7925 (m-80)
REVERT: A  193 ARG cc_start: 0.8416 (mmp80) cc_final: 0.8058 (mmp80)
REVERT: A  460 GLU cc_start: 0.8352 (pm20) cc_final: 0.8051 (pm20)
REVERT: A  724 LYS cc_start: 0.8878 (mmpt) cc_final: 0.8615 (mmpt)
REVERT: A  788 ASP cc_start: 0.8172 (t70) cc_final: 0.7799 (t0)
REVERT: A  824 ARG cc_start: 0.8326 (mmm-85) cc_final: 0.7928 (ttm110)
REVERT: A  834 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7212 (pm20)
REVERT: A 1099 ASP cc_start: 0.8996 (m-30) cc_final: 0.8745 (m-30)
REVERT: A 1124 ASP cc_start: 0.8979 (t70) cc_final: 0.8597 (t0)
REVERT: A 1225 MET cc_start: 0.8916 (mmt) cc_final: 0.8500 (mmt)
REVERT: A 1313 GLU cc_start: 0.8487 (tp30) cc_final: 0.8210 (mm-30)
REVERT: A 1442 GLU cc_start: 0.8130 (mp0) cc_final: 0.7773 (mp0)
REVERT: B  554 ASP cc_start: 0.8586 (m-30) cc_final: 0.8263 (m-30)
REVERT: B  606 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7860 (mm-40)
REVERT: B  665 LYS cc_start: 0.8297 (tttm) cc_final: 0.8066 (ttmm)
REVERT: B  669 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8044 (mmt90)
REVERT: C  564 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7816 (tp)
REVERT: C  577 MET cc_start: 0.8242 (tmm) cc_final: 0.7392 (tmt)
REVERT: E  581 LYS cc_start: 0.8630 (tppt) cc_final: 0.8275 (mppt)
  outliers start: 28
  outliers final: 16
  residues processed: 252
  average time/residue: 1.3251
  time to fit residues: 363.1640
Evaluate side-chains
  253 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 235
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  823 THR
Chi-restraints excluded: chain A residue  834 GLU
Chi-restraints excluded: chain A residue  922 GLU
Chi-restraints excluded: chain A residue 1203 MET
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain C residue  564 LEU
Chi-restraints excluded: chain C residue  573 SER
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain E residue  551 GLU
Chi-restraints excluded: chain E residue  560 THR
Chi-restraints excluded: chain E residue  561 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 152 optimal weight:    0.7980
   chunk 155 optimal weight:   30.0000
   chunk 6 optimal weight:    3.9990
   chunk 142 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 94 optimal weight:    3.9990
   chunk 141 optimal weight:    0.4980
   chunk 41 optimal weight:    0.5980
   chunk 87 optimal weight:    0.0670
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A 427 HIS
A1125 ASN
A1264 HIS
B 648 ASN
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 561 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.118783 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.077371 restraints weight = 43419.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 4.11
r_work: 0.2785 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2787 r_free = 0.2787    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13285  Z= 0.127
  Angle     :  0.625  10.483  17921  Z= 0.318
  Chirality :  0.042   0.176   2049
  Planarity :  0.004   0.060   2275
  Dihedral  :  4.168  22.165   1754
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 16.81 %
    Favored  : 81.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.82 (0.22), residues: 1604
  helix:  2.02 (0.18), residues: 917
  sheet:  0.25 (0.52), residues: 97
  loop :  0.17 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A1306 
 HIS   0.009   0.001   HIS E 535 
 PHE   0.016   0.001   PHE A 399 
 TYR   0.010   0.001   TYR A 389 
 ARG   0.014   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03994 (  747)
  hydrogen bonds       : angle       4.36083 ( 2150)
  metal coordination   : bond        0.00308 (    7)
  metal coordination   : angle       2.87470 (    1)
  covalent geometry    : bond        0.00284 (13278)
  covalent geometry    : angle       0.62417 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 241
  time to evaluate  : 1.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 ASP cc_start: 0.8669 (t0) cc_final: 0.8264 (t0)
REVERT: A   81 LYS cc_start: 0.9239 (mtmm) cc_final: 0.9025 (mppt)
REVERT: A  192 PHE cc_start: 0.8455 (m-80) cc_final: 0.7919 (m-80)
REVERT: A  193 ARG cc_start: 0.8422 (mmp80) cc_final: 0.8053 (mmp80)
REVERT: A  460 GLU cc_start: 0.8345 (pm20) cc_final: 0.8037 (pm20)
REVERT: A  724 LYS cc_start: 0.8860 (mmpt) cc_final: 0.8581 (mmpt)
REVERT: A  788 ASP cc_start: 0.8162 (t70) cc_final: 0.7776 (t0)
REVERT: A  824 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7933 (ttm110)
REVERT: A  834 GLU cc_start: 0.7551 (OUTLIER) cc_final: 0.7292 (pm20)
REVERT: A 1124 ASP cc_start: 0.9036 (t70) cc_final: 0.8715 (t0)
REVERT: A 1225 MET cc_start: 0.8910 (mmt) cc_final: 0.8488 (mmt)
REVERT: A 1313 GLU cc_start: 0.8495 (tp30) cc_final: 0.8220 (mm-30)
REVERT: A 1440 ASP cc_start: 0.8291 (m-30) cc_final: 0.7896 (m-30)
REVERT: A 1442 GLU cc_start: 0.8094 (mp0) cc_final: 0.7737 (mp0)
REVERT: B  554 ASP cc_start: 0.8568 (m-30) cc_final: 0.8243 (m-30)
REVERT: B  606 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7847 (mm-40)
REVERT: B  669 ARG cc_start: 0.8419 (mtt-85) cc_final: 0.8080 (mmt90)
REVERT: B  695 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8121 (mp10)
REVERT: C  564 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7925 (tp)
REVERT: C  577 MET cc_start: 0.8281 (tmm) cc_final: 0.7501 (tmt)
REVERT: E  581 LYS cc_start: 0.8600 (tppt) cc_final: 0.8265 (mppt)
  outliers start: 21
  outliers final: 11
  residues processed: 247
  average time/residue: 1.3882
  time to fit residues: 372.5874
Evaluate side-chains
  247 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 233
  time to evaluate  : 1.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  834 GLU
Chi-restraints excluded: chain A residue  922 GLU
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain B residue  695 GLN
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain C residue  564 LEU
Chi-restraints excluded: chain C residue  573 SER
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain E residue  551 GLU
Chi-restraints excluded: chain E residue  561 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 145 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   chunk 136 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A 427 HIS
A1264 HIS
B 648 ASN
D 561 ASN
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 561 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.117958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.077060 restraints weight = 35583.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 3.76
r_work: 0.2786 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13285  Z= 0.145
  Angle     :  0.631  11.345  17921  Z= 0.322
  Chirality :  0.043   0.189   2049
  Planarity :  0.004   0.063   2275
  Dihedral  :  4.190  22.313   1754
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 17.43 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.80 (0.21), residues: 1604
  helix:  2.00 (0.18), residues: 916
  sheet:  0.20 (0.51), residues: 97
  loop :  0.18 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A1306 
 HIS   0.009   0.001   HIS E 535 
 PHE   0.017   0.001   PHE A 399 
 TYR   0.011   0.001   TYR A 284 
 ARG   0.015   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04089 (  747)
  hydrogen bonds       : angle       4.39708 ( 2150)
  metal coordination   : bond        0.00390 (    7)
  metal coordination   : angle       2.17910 (    1)
  covalent geometry    : bond        0.00333 (13278)
  covalent geometry    : angle       0.63109 (17920)

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

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

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3208 Ramachandran restraints generated.
    1604 Oldfield, 0 Emsley, 1604 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 236
  time to evaluate  : 1.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.9232 (mtmm) cc_final: 0.9020 (mppt)
REVERT: A  192 PHE cc_start: 0.8470 (m-80) cc_final: 0.7930 (m-80)
REVERT: A  193 ARG cc_start: 0.8408 (mmp80) cc_final: 0.8043 (mmp80)
REVERT: A  460 GLU cc_start: 0.8370 (pm20) cc_final: 0.8059 (pm20)
REVERT: A  724 LYS cc_start: 0.8870 (mmpt) cc_final: 0.8604 (mmpt)
REVERT: A  788 ASP cc_start: 0.8209 (t70) cc_final: 0.7842 (t0)
REVERT: A  824 ARG cc_start: 0.8333 (mmm-85) cc_final: 0.7938 (ttm110)
REVERT: A  834 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7275 (pm20)
REVERT: A 1099 ASP cc_start: 0.8994 (m-30) cc_final: 0.8772 (m-30)
REVERT: A 1124 ASP cc_start: 0.9045 (t70) cc_final: 0.8724 (t0)
REVERT: A 1225 MET cc_start: 0.8900 (mmt) cc_final: 0.8480 (mmt)
REVERT: A 1313 GLU cc_start: 0.8494 (tp30) cc_final: 0.8213 (mm-30)
REVERT: A 1440 ASP cc_start: 0.8297 (m-30) cc_final: 0.7960 (m-30)
REVERT: A 1442 GLU cc_start: 0.8096 (mp0) cc_final: 0.7743 (mp0)
REVERT: B  554 ASP cc_start: 0.8535 (m-30) cc_final: 0.8211 (m-30)
REVERT: B  606 GLN cc_start: 0.8257 (mm-40) cc_final: 0.7853 (mm-40)
REVERT: B  695 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8153 (mp10)
REVERT: C  564 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7869 (tp)
REVERT: C  577 MET cc_start: 0.8293 (tmm) cc_final: 0.7526 (tmt)
REVERT: D  555 ARG cc_start: 0.8649 (mtp180) cc_final: 0.8252 (mtm-85)
REVERT: E  559 LYS cc_start: 0.9183 (tmmt) cc_final: 0.8726 (pptt)
REVERT: E  581 LYS cc_start: 0.8600 (tppt) cc_final: 0.8240 (mppt)
  outliers start: 17
  outliers final: 12
  residues processed: 241
  average time/residue: 1.3677
  time to fit residues: 357.6696
Evaluate side-chains
  243 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 228
  time to evaluate  : 1.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  834 GLU
Chi-restraints excluded: chain A residue  922 GLU
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain A residue 1445 ILE
Chi-restraints excluded: chain B residue  695 GLN
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain C residue  564 LEU
Chi-restraints excluded: chain C residue  573 SER
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain E residue  551 GLU
Chi-restraints excluded: chain E residue  561 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 149 optimal weight:    8.9990
   chunk 123 optimal weight:    0.9990
   chunk 132 optimal weight:    6.9990
   chunk 155 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 157 optimal weight:   10.0000
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
A1264 HIS
B 648 ASN
** C 570 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 561 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.113667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.073668 restraints weight = 25662.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 3.19
r_work: 0.2731 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056  13285  Z= 0.287
  Angle     :  0.721  13.198  17921  Z= 0.367
  Chirality :  0.047   0.204   2049
  Planarity :  0.005   0.066   2275
  Dihedral  :  4.504  23.650   1754
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.15 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    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:  1.47 (0.21), residues: 1604
  helix:  1.72 (0.17), residues: 919
  sheet: -0.27 (0.51), residues: 90
  loop :  0.10 (0.25), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A1306 
 HIS   0.009   0.001   HIS D 535 
 PHE   0.021   0.002   PHE A 399 
 TYR   0.019   0.002   TYR A 529 
 ARG   0.014   0.001   ARG A 202 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04956 (  747)
  hydrogen bonds       : angle       4.66408 ( 2150)
  metal coordination   : bond        0.01589 (    7)
  metal coordination   : angle       0.53148 (    1)
  covalent geometry    : bond        0.00682 (13278)
  covalent geometry    : angle       0.72079 (17920)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 15801.96 seconds
wall clock time: 274 minutes 12.34 seconds (16452.34 seconds total)