Starting phenix.real_space_refine
on Thu Sep 18 01:52:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iv9_60922/09_2025/9iv9_60922.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iv9_60922/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iv9_60922/09_2025/9iv9_60922.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iv9_60922/09_2025/9iv9_60922.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iv9_60922/09_2025/9iv9_60922.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iv9_60922/09_2025/9iv9_60922.map"
  }
  resolution = 2.31
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.056
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.70, per 1000 atoms: 0.36
  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: 0.85
  Conformation dependent library (CDL) restraints added in 987.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  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: 0.61
  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: 2.36

  Time building geometry restraints manager: 1.12 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:             0.990
  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:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     16.450
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.050
  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:7.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.280
-------------------------------------------------------------------------------
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 : 3.69
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.010   0.001   ARG B 669 
 TYR   0.018   0.002   TYR A 389 
 PHE   0.020   0.002   PHE A 399 
 TRP   0.017   0.002   TRP A1306 
 HIS   0.014   0.001   HIS E 535 

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

*********************** 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  : 0.500 
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: 0.7706 (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 1225 MET cc_start: 0.8885 (mmt) cc_final: 0.8538 (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: 0.6797
  time to fit residues: 227.0199
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  : 0.553 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:   20.0000
   overall best weight:    0.8582

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.120398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.079849 restraints weight = 37131.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 3.81
r_work: 0.2828 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2830
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2830 r_free = 0.2830    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  13285  Z= 0.143
  Angle     :  0.607  11.118  17921  Z= 0.313
  Chirality :  0.043   0.166   2049
  Planarity :  0.005   0.060   2275
  Dihedral  :  5.297  91.306   1758
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 12.05 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.21), residues: 1604
  helix:  1.51 (0.18), residues: 905
  sheet:  0.47 (0.54), residues: 90
  loop : -0.03 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 675 
 TYR   0.015   0.001   TYR A 793 
 PHE   0.017   0.001   PHE A 399 
 TRP   0.012   0.001   TRP A1248 
 HIS   0.009   0.001   HIS E 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 (13278)
  covalent geometry    : angle       0.60584 (17920)
  hydrogen bonds       : bond        0.04421 (  747)
  hydrogen bonds       : angle       4.60904 ( 2150)
  metal coordination   : bond        0.00529 (    7)
  metal coordination   : angle       4.43761 (    1)

*********************** 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
  267 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 251
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 ARG cc_start: 0.8310 (ttm110) cc_final: 0.8101 (ttm110)
REVERT: A   59 LYS cc_start: 0.9024 (mmtp) cc_final: 0.8688 (mttt)
REVERT: A  192 PHE cc_start: 0.8524 (m-80) cc_final: 0.8166 (m-80)
REVERT: A  460 GLU cc_start: 0.8254 (pm20) cc_final: 0.7981 (pm20)
REVERT: A  724 LYS cc_start: 0.8809 (mmpt) cc_final: 0.8486 (mmpt)
REVERT: A  788 ASP cc_start: 0.8088 (t70) cc_final: 0.7719 (t0)
REVERT: A  834 GLU cc_start: 0.7340 (pm20) cc_final: 0.6983 (pm20)
REVERT: A  907 LYS cc_start: 0.9089 (tttt) cc_final: 0.8805 (tttp)
REVERT: A 1066 GLN cc_start: 0.8313 (pp30) cc_final: 0.8027 (pp30)
REVERT: A 1099 ASP cc_start: 0.8964 (m-30) cc_final: 0.8716 (m-30)
REVERT: A 1124 ASP cc_start: 0.8862 (t70) cc_final: 0.8336 (t0)
REVERT: A 1225 MET cc_start: 0.8853 (mmt) cc_final: 0.8392 (mmt)
REVERT: A 1313 GLU cc_start: 0.8572 (tp30) cc_final: 0.8352 (mm-30)
REVERT: B  606 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7797 (mm-40)
REVERT: B  669 ARG cc_start: 0.8463 (mtt-85) cc_final: 0.8247 (mtt90)
REVERT: B  699 ASN cc_start: 0.8727 (m110) cc_final: 0.8468 (m-40)
REVERT: C  550 LEU cc_start: 0.8752 (mt) cc_final: 0.8355 (tt)
REVERT: C  577 MET cc_start: 0.8133 (tmm) cc_final: 0.7529 (tmt)
  outliers start: 16
  outliers final: 4
  residues processed: 255
  average time/residue: 0.6711
  time to fit residues: 184.4199
Evaluate side-chains
  237 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 233
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 GLU
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1231 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 157 optimal weight:    9.9990
   chunk 84 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 113 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 159 optimal weight:    0.9980
   chunk 136 optimal weight:    4.9990
   chunk 111 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   overall best weight:    1.1386

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.119212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.078503 restraints weight = 37166.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.2962 rms_B_bonded: 3.81
r_work: 0.2789 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    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 = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13285  Z= 0.158
  Angle     :  0.595   9.779  17921  Z= 0.304
  Chirality :  0.043   0.176   2049
  Planarity :  0.004   0.055   2275
  Dihedral  :  4.276  18.000   1754
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.66 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.21), residues: 1604
  helix:  1.89 (0.18), residues: 905
  sheet:  0.36 (0.54), residues: 90
  loop :  0.02 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 202 
 TYR   0.013   0.001   TYR A 793 
 PHE   0.018   0.001   PHE A 399 
 TRP   0.014   0.001   TRP A1306 
 HIS   0.009   0.001   HIS D 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (13278)
  covalent geometry    : angle       0.59467 (17920)
  hydrogen bonds       : bond        0.04307 (  747)
  hydrogen bonds       : angle       4.45735 ( 2150)
  metal coordination   : bond        0.00593 (    7)
  metal coordination   : angle       2.97221 (    1)

*********************** 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
  263 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 239
  time to evaluate  : 0.519 
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: 0.9045 (mmtp) cc_final: 0.8766 (mttt)
REVERT: A   81 LYS cc_start: 0.9233 (mtmm) cc_final: 0.9015 (mppt)
REVERT: A  192 PHE cc_start: 0.8484 (m-80) cc_final: 0.8052 (m-80)
REVERT: A  381 MET cc_start: 0.9042 (mtm) cc_final: 0.8842 (ttp)
REVERT: A  460 GLU cc_start: 0.8275 (pm20) cc_final: 0.8009 (pm20)
REVERT: A  724 LYS cc_start: 0.8842 (mmpt) cc_final: 0.8558 (mmpt)
REVERT: A  788 ASP cc_start: 0.8131 (t70) cc_final: 0.7760 (t0)
REVERT: A  799 GLU cc_start: 0.8095 (mp0) cc_final: 0.7866 (mp0)
REVERT: A  834 GLU cc_start: 0.7360 (pm20) cc_final: 0.7041 (pm20)
REVERT: A  843 HIS cc_start: 0.8082 (t-90) cc_final: 0.7803 (t-170)
REVERT: A 1099 ASP cc_start: 0.8961 (m-30) cc_final: 0.8717 (m-30)
REVERT: A 1124 ASP cc_start: 0.8895 (t70) cc_final: 0.8431 (t0)
REVERT: A 1225 MET cc_start: 0.8919 (mmt) cc_final: 0.8499 (mmt)
REVERT: A 1295 ARG cc_start: 0.8095 (mtt90) cc_final: 0.7887 (mtt90)
REVERT: A 1313 GLU cc_start: 0.8580 (tp30) cc_final: 0.8344 (mm-30)
REVERT: A 1392 TYR cc_start: 0.7017 (m-80) cc_final: 0.6817 (m-80)
REVERT: B  554 ASP cc_start: 0.8600 (m-30) cc_final: 0.8264 (m-30)
REVERT: B  606 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7878 (mm-40)
REVERT: B  669 ARG cc_start: 0.8392 (mtt-85) cc_final: 0.8133 (mmt90)
REVERT: B  699 ASN cc_start: 0.8818 (m110) cc_final: 0.8574 (m-40)
REVERT: C  550 LEU cc_start: 0.8835 (mt) cc_final: 0.8459 (tt)
REVERT: C  577 MET cc_start: 0.8211 (tmm) cc_final: 0.7533 (tmt)
  outliers start: 24
  outliers final: 11
  residues processed: 248
  average time/residue: 0.6617
  time to fit residues: 177.1069
Evaluate side-chains
  238 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 227
  time to evaluate  : 0.501 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  388 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 1426 ASP
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain D residue  557 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 158 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 109 optimal weight:    5.9990
   chunk 127 optimal weight:    8.9990
   chunk 40 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 140 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0000
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 188 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 = 0.3628 r_free = 0.3628 target = 0.118021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.076991 restraints weight = 40678.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 3.95
r_work: 0.2760 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2760
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2760 r_free = 0.2760    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 = 0.2760 r_free = 0.2760    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2760
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13285  Z= 0.177
  Angle     :  0.600  10.239  17921  Z= 0.306
  Chirality :  0.044   0.167   2049
  Planarity :  0.004   0.051   2275
  Dihedral  :  4.298  19.871   1754
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 13.68 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.21), residues: 1604
  helix:  1.96 (0.18), residues: 909
  sheet:  0.32 (0.54), residues: 90
  loop :  0.08 (0.25), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 202 
 TYR   0.013   0.001   TYR A 862 
 PHE   0.018   0.001   PHE A 399 
 TRP   0.016   0.002   TRP A1306 
 HIS   0.008   0.001   HIS E 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 (13278)
  covalent geometry    : angle       0.60019 (17920)
  hydrogen bonds       : bond        0.04356 (  747)
  hydrogen bonds       : angle       4.44398 ( 2150)
  metal coordination   : bond        0.00733 (    7)
  metal coordination   : angle       1.86225 (    1)

*********************** 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
  263 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 240
  time to evaluate  : 0.509 
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   81 LYS cc_start: 0.9240 (mtmm) cc_final: 0.9039 (mppt)
REVERT: A  192 PHE cc_start: 0.8467 (m-80) cc_final: 0.8015 (m-80)
REVERT: A  460 GLU cc_start: 0.8270 (pm20) cc_final: 0.8028 (pm20)
REVERT: A  724 LYS cc_start: 0.8856 (mmpt) cc_final: 0.8587 (mmpt)
REVERT: A  788 ASP cc_start: 0.8133 (t70) cc_final: 0.7764 (t0)
REVERT: A  799 GLU cc_start: 0.8099 (mp0) cc_final: 0.7832 (mp0)
REVERT: A  834 GLU cc_start: 0.7334 (pm20) cc_final: 0.6977 (pm20)
REVERT: A 1099 ASP cc_start: 0.8976 (m-30) cc_final: 0.8720 (m-30)
REVERT: A 1124 ASP cc_start: 0.8953 (t70) cc_final: 0.8480 (t0)
REVERT: A 1225 MET cc_start: 0.8914 (mmt) cc_final: 0.8488 (mmt)
REVERT: A 1313 GLU cc_start: 0.8559 (tp30) cc_final: 0.8322 (mm-30)
REVERT: B  554 ASP cc_start: 0.8595 (m-30) cc_final: 0.8257 (m-30)
REVERT: B  606 GLN cc_start: 0.8260 (mm-40) cc_final: 0.7900 (mm-40)
REVERT: B  699 ASN cc_start: 0.8766 (m110) cc_final: 0.8515 (m-40)
REVERT: C  564 LEU cc_start: 0.8197 (mm) cc_final: 0.7981 (tp)
REVERT: C  577 MET cc_start: 0.8222 (tmm) cc_final: 0.7453 (tmt)
REVERT: D  555 ARG cc_start: 0.8556 (mpp80) cc_final: 0.8229 (mpp80)
REVERT: D  575 MET cc_start: 0.8687 (mtp) cc_final: 0.7964 (mtp)
  outliers start: 23
  outliers final: 10
  residues processed: 249
  average time/residue: 0.6721
  time to fit residues: 180.7920
Evaluate side-chains
  242 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 232
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue  388 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 B residue  597 VAL
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain D residue  557 LEU
Chi-restraints excluded: chain E residue  547 ILE
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 69 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 157 optimal weight:    9.9990
   chunk 68 optimal weight:    0.0040
   chunk 56 optimal weight:    0.7980
   chunk 130 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 135 optimal weight:    3.9990
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.6392

-------------------------------------------------------------------------------
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
B 648 ASN
** 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 = 0.3630 r_free = 0.3630 target = 0.118789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.078293 restraints weight = 32183.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.2977 rms_B_bonded: 3.59
r_work: 0.2808 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2810
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2810
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.1851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13285  Z= 0.127
  Angle     :  0.582   9.267  17921  Z= 0.296
  Chirality :  0.042   0.190   2049
  Planarity :  0.004   0.049   2275
  Dihedral  :  4.198  18.629   1754
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.70 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.21), residues: 1604
  helix:  2.10 (0.18), residues: 908
  sheet:  0.42 (0.52), residues: 97
  loop :  0.13 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 202 
 TYR   0.010   0.001   TYR A 284 
 PHE   0.017   0.001   PHE A 399 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.008   0.001   HIS D 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (13278)
  covalent geometry    : angle       0.58110 (17920)
  hydrogen bonds       : bond        0.04082 (  747)
  hydrogen bonds       : angle       4.33175 ( 2150)
  metal coordination   : bond        0.00334 (    7)
  metal coordination   : angle       3.12096 (    1)

*********************** 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
  272 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 249
  time to evaluate  : 0.351 
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: 0.9034 (mmtp) cc_final: 0.8771 (mttt)
REVERT: A   81 LYS cc_start: 0.9224 (mtmm) cc_final: 0.9018 (mppt)
REVERT: A  192 PHE cc_start: 0.8474 (m-80) cc_final: 0.7975 (m-80)
REVERT: A  460 GLU cc_start: 0.8255 (pm20) cc_final: 0.7997 (pm20)
REVERT: A  724 LYS cc_start: 0.8836 (mmpt) cc_final: 0.8549 (mmpt)
REVERT: A  788 ASP cc_start: 0.8085 (t70) cc_final: 0.7713 (t0)
REVERT: A  893 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8917 (mtpp)
REVERT: A 1099 ASP cc_start: 0.8959 (m-30) cc_final: 0.8696 (m-30)
REVERT: A 1124 ASP cc_start: 0.8921 (t70) cc_final: 0.8480 (t0)
REVERT: A 1225 MET cc_start: 0.8925 (mmt) cc_final: 0.8511 (mmt)
REVERT: A 1295 ARG cc_start: 0.8000 (mtt180) cc_final: 0.7526 (mtt180)
REVERT: A 1313 GLU cc_start: 0.8504 (tp30) cc_final: 0.8229 (mm-30)
REVERT: A 1440 ASP cc_start: 0.8272 (m-30) cc_final: 0.7985 (m-30)
REVERT: A 1442 GLU cc_start: 0.8172 (mp0) cc_final: 0.7842 (mp0)
REVERT: B  554 ASP cc_start: 0.8624 (m-30) cc_final: 0.8280 (m-30)
REVERT: B  606 GLN cc_start: 0.8282 (mm-40) cc_final: 0.7906 (mm-40)
REVERT: B  675 ARG cc_start: 0.8468 (mmm-85) cc_final: 0.7985 (mmm-85)
REVERT: C  564 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8098 (tp)
REVERT: C  577 MET cc_start: 0.8262 (tmm) cc_final: 0.7476 (tmt)
REVERT: D  547 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8658 (tp)
REVERT: D  575 MET cc_start: 0.8710 (mtp) cc_final: 0.8042 (mtp)
REVERT: E  581 LYS cc_start: 0.8618 (tppt) cc_final: 0.8252 (mppt)
  outliers start: 23
  outliers final: 14
  residues processed: 259
  average time/residue: 0.6441
  time to fit residues: 180.6829
Evaluate side-chains
  246 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 230
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
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 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain A residue 1426 ASP
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain C residue  542 GLU
Chi-restraints excluded: chain C residue  564 LEU
Chi-restraints excluded: chain D residue  547 ILE
Chi-restraints excluded: chain D residue  555 ARG
Chi-restraints excluded: chain D residue  564 LEU
Chi-restraints excluded: chain E residue  547 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 152 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 70 optimal weight:    5.9990
   chunk 147 optimal weight:    0.9980
   chunk 150 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 158 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 188 GLN
** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.117348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.075930 restraints weight = 40723.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 4.00
r_work: 0.2760 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2762
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.2003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13285  Z= 0.165
  Angle     :  0.610   9.620  17921  Z= 0.309
  Chirality :  0.043   0.153   2049
  Planarity :  0.004   0.054   2275
  Dihedral  :  4.216  19.123   1754
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.25 %
    Favored  : 82.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.21), residues: 1604
  helix:  2.10 (0.18), residues: 908
  sheet:  0.29 (0.54), residues: 90
  loop :  0.16 (0.25), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 202 
 TYR   0.013   0.001   TYR A 793 
 PHE   0.018   0.001   PHE A 726 
 TRP   0.011   0.001   TRP A 754 
 HIS   0.009   0.001   HIS E 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (13278)
  covalent geometry    : angle       0.61023 (17920)
  hydrogen bonds       : bond        0.04231 (  747)
  hydrogen bonds       : angle       4.36476 ( 2150)
  metal coordination   : bond        0.00589 (    7)
  metal coordination   : angle       1.83451 (    1)

*********************** 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
  259 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 233
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.9243 (mtmm) cc_final: 0.9025 (mppt)
REVERT: A  192 PHE cc_start: 0.8452 (m-80) cc_final: 0.8000 (m-80)
REVERT: A  460 GLU cc_start: 0.8318 (pm20) cc_final: 0.8046 (pm20)
REVERT: A  724 LYS cc_start: 0.8853 (mmpt) cc_final: 0.8562 (mmpt)
REVERT: A  788 ASP cc_start: 0.8146 (t70) cc_final: 0.7761 (t0)
REVERT: A  834 GLU cc_start: 0.7449 (mp0) cc_final: 0.7218 (pm20)
REVERT: A  893 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8913 (mtpp)
REVERT: A 1099 ASP cc_start: 0.8977 (m-30) cc_final: 0.8736 (m-30)
REVERT: A 1124 ASP cc_start: 0.8972 (t70) cc_final: 0.8577 (t0)
REVERT: A 1225 MET cc_start: 0.8913 (mmt) cc_final: 0.8493 (mmt)
REVERT: A 1295 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7536 (mtt180)
REVERT: A 1313 GLU cc_start: 0.8512 (tp30) cc_final: 0.8237 (mm-30)
REVERT: A 1442 GLU cc_start: 0.8200 (mp0) cc_final: 0.7847 (mp0)
REVERT: B  554 ASP cc_start: 0.8643 (m-30) cc_final: 0.8337 (m-30)
REVERT: B  606 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7859 (mm-40)
REVERT: C  564 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8026 (tp)
REVERT: C  577 MET cc_start: 0.8290 (tmm) cc_final: 0.7478 (tmt)
REVERT: D  555 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.8349 (mtm-85)
REVERT: E  581 LYS cc_start: 0.8582 (tppt) cc_final: 0.8262 (mppt)
  outliers start: 26
  outliers final: 13
  residues processed: 243
  average time/residue: 0.6332
  time to fit residues: 166.4435
Evaluate side-chains
  246 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 231
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
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  716 SER
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 1426 ASP
Chi-restraints excluded: chain B residue  597 VAL
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 D residue  555 ARG
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 8 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 47 optimal weight:    0.8980
   chunk 98 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0040
   chunk 30 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.6392

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS
B 561 ASN
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 = 0.3629 r_free = 0.3629 target = 0.118692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.077872 restraints weight = 36042.488|
|-----------------------------------------------------------------------------|
r_work (start): 0.2973 rms_B_bonded: 3.78
r_work: 0.2800 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2802
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2802 r_free = 0.2802    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 = 0.2802 r_free = 0.2802    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2802
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.2014

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= 0.127
  Angle     :  0.594  11.638  17921  Z= 0.301
  Chirality :  0.042   0.161   2049
  Planarity :  0.004   0.054   2275
  Dihedral  :  4.152  18.965   1754
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.52 %
    Favored  : 82.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.22), residues: 1604
  helix:  2.13 (0.18), residues: 909
  sheet:  0.40 (0.52), residues: 97
  loop :  0.18 (0.26), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 202 
 TYR   0.012   0.001   TYR A 793 
 PHE   0.016   0.001   PHE A 399 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.009   0.001   HIS E 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (13278)
  covalent geometry    : angle       0.59387 (17920)
  hydrogen bonds       : bond        0.04023 (  747)
  hydrogen bonds       : angle       4.30256 ( 2150)
  metal coordination   : bond        0.00343 (    7)
  metal coordination   : angle       2.94419 (    1)

*********************** 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
  263 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 238
  time to evaluate  : 0.538 
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: 0.9236 (mtmm) cc_final: 0.9023 (mppt)
REVERT: A  192 PHE cc_start: 0.8447 (m-80) cc_final: 0.7914 (m-80)
REVERT: A  460 GLU cc_start: 0.8337 (pm20) cc_final: 0.8026 (pm20)
REVERT: A  724 LYS cc_start: 0.8842 (mmpt) cc_final: 0.8576 (mmpt)
REVERT: A  788 ASP cc_start: 0.8153 (t70) cc_final: 0.7758 (t0)
REVERT: A  834 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7087 (pm20)
REVERT: A  893 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8903 (mtpp)
REVERT: A 1099 ASP cc_start: 0.8972 (m-30) cc_final: 0.8722 (m-30)
REVERT: A 1124 ASP cc_start: 0.9022 (t70) cc_final: 0.8624 (t0)
REVERT: A 1225 MET cc_start: 0.8912 (mmt) cc_final: 0.8484 (mmt)
REVERT: A 1295 ARG cc_start: 0.7974 (mtt180) cc_final: 0.7521 (mtt180)
REVERT: A 1313 GLU cc_start: 0.8499 (tp30) cc_final: 0.8219 (mm-30)
REVERT: A 1440 ASP cc_start: 0.8258 (m-30) cc_final: 0.7899 (m-30)
REVERT: A 1442 GLU cc_start: 0.8147 (mp0) cc_final: 0.7796 (mp0)
REVERT: B  549 LYS cc_start: 0.8544 (tttm) cc_final: 0.8264 (tttt)
REVERT: B  554 ASP cc_start: 0.8678 (m-30) cc_final: 0.8373 (m-30)
REVERT: B  606 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7911 (mm-40)
REVERT: C  550 LEU cc_start: 0.8713 (mt) cc_final: 0.8475 (mt)
REVERT: C  554 ASP cc_start: 0.9134 (t0) cc_final: 0.8933 (m-30)
REVERT: C  564 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8008 (tp)
REVERT: C  577 MET cc_start: 0.8267 (tmm) cc_final: 0.7586 (tmt)
REVERT: D  555 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8300 (mtm-85)
REVERT: E  581 LYS cc_start: 0.8626 (tppt) cc_final: 0.8304 (mppt)
  outliers start: 25
  outliers final: 11
  residues processed: 247
  average time/residue: 0.6324
  time to fit residues: 168.9983
Evaluate side-chains
  245 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 231
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
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  716 SER
Chi-restraints excluded: chain A residue  834 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 B residue  597 VAL
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 D residue  555 ARG
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 1 optimal weight:    6.9990
   chunk 124 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 150 optimal weight:   10.0000
   chunk 126 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 88 optimal weight:    2.9990
   chunk 59 optimal weight:    9.9990
   chunk 118 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1264 HIS
B 648 ASN
C 570 HIS
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 = 0.3606 r_free = 0.3606 target = 0.116782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.076442 restraints weight = 30278.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 3.46
r_work: 0.2780 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2780
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2782
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    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 = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13285  Z= 0.166
  Angle     :  0.622  13.456  17921  Z= 0.315
  Chirality :  0.043   0.157   2049
  Planarity :  0.004   0.059   2275
  Dihedral  :  4.194  19.119   1754
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.59 %
    Favored  : 82.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.88 (0.21), residues: 1604
  helix:  2.09 (0.18), residues: 909
  sheet:  0.21 (0.54), residues: 90
  loop :  0.19 (0.26), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 202 
 TYR   0.013   0.001   TYR A 862 
 PHE   0.021   0.001   PHE A 726 
 TRP   0.011   0.001   TRP A 173 
 HIS   0.009   0.001   HIS E 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (13278)
  covalent geometry    : angle       0.62236 (17920)
  hydrogen bonds       : bond        0.04241 (  747)
  hydrogen bonds       : angle       4.37448 ( 2150)
  metal coordination   : bond        0.00627 (    7)
  metal coordination   : angle       1.58530 (    1)

*********************** 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
  260 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 239
  time to evaluate  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.9223 (mtmm) cc_final: 0.9008 (mppt)
REVERT: A  192 PHE cc_start: 0.8456 (m-80) cc_final: 0.7926 (m-80)
REVERT: A  193 ARG cc_start: 0.8425 (mmp80) cc_final: 0.8129 (mmp80)
REVERT: A  460 GLU cc_start: 0.8342 (pm20) cc_final: 0.8055 (pm20)
REVERT: A  724 LYS cc_start: 0.8861 (mmpt) cc_final: 0.8573 (mmpt)
REVERT: A  788 ASP cc_start: 0.8179 (t70) cc_final: 0.7805 (t0)
REVERT: A  834 GLU cc_start: 0.7479 (mp0) cc_final: 0.7139 (pm20)
REVERT: A  893 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8910 (mtpp)
REVERT: A 1099 ASP cc_start: 0.8976 (m-30) cc_final: 0.8693 (m-30)
REVERT: A 1124 ASP cc_start: 0.9044 (t70) cc_final: 0.8658 (t0)
REVERT: A 1225 MET cc_start: 0.8895 (mmt) cc_final: 0.8467 (mmt)
REVERT: A 1295 ARG cc_start: 0.8002 (mtt180) cc_final: 0.7553 (mtt180)
REVERT: A 1313 GLU cc_start: 0.8493 (tp30) cc_final: 0.8217 (mm-30)
REVERT: A 1442 GLU cc_start: 0.8185 (mp0) cc_final: 0.7874 (mp0)
REVERT: B  554 ASP cc_start: 0.8677 (m-30) cc_final: 0.8368 (m-30)
REVERT: B  606 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7864 (mm-40)
REVERT: B  669 ARG cc_start: 0.8393 (mtt-85) cc_final: 0.8034 (mmt90)
REVERT: C  564 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7920 (tp)
REVERT: C  577 MET cc_start: 0.8253 (tmm) cc_final: 0.7517 (tmt)
REVERT: D  555 ARG cc_start: 0.8735 (mpp80) cc_final: 0.8497 (mtp180)
REVERT: E  581 LYS cc_start: 0.8639 (tppt) cc_final: 0.8337 (mppt)
  outliers start: 21
  outliers final: 14
  residues processed: 246
  average time/residue: 0.6389
  time to fit residues: 169.9408
Evaluate side-chains
  247 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 232
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  348 ASP
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 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 B residue  597 VAL
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 E residue  551 GLU
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 33 optimal weight:    0.6980
   chunk 132 optimal weight:    5.9990
   chunk 104 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 133 optimal weight:    0.3980
   chunk 63 optimal weight:    1.9990
   chunk 130 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 136 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1074 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 = 0.3623 r_free = 0.3623 target = 0.118307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.077326 restraints weight = 40901.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.2963 rms_B_bonded: 3.94
r_work: 0.2786 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
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: 0.8108
moved from start:          0.2165

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= 0.134
  Angle     :  0.624  14.340  17921  Z= 0.317
  Chirality :  0.042   0.163   2049
  Planarity :  0.004   0.060   2275
  Dihedral  :  4.177  21.321   1754
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.13 %
    Favored  : 82.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.22), residues: 1604
  helix:  2.13 (0.18), residues: 910
  sheet:  0.29 (0.52), residues: 97
  loop :  0.20 (0.26), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 202 
 TYR   0.010   0.001   TYR A 389 
 PHE   0.016   0.001   PHE A 399 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.009   0.001   HIS E 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (13278)
  covalent geometry    : angle       0.62373 (17920)
  hydrogen bonds       : bond        0.04025 (  747)
  hydrogen bonds       : angle       4.33243 ( 2150)
  metal coordination   : bond        0.00331 (    7)
  metal coordination   : angle       2.75107 (    1)

*********************** 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
  258 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 240
  time to evaluate  : 0.480 
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   81 LYS cc_start: 0.9236 (mtmm) cc_final: 0.9021 (mppt)
REVERT: A  192 PHE cc_start: 0.8454 (m-80) cc_final: 0.7908 (m-80)
REVERT: A  193 ARG cc_start: 0.8452 (mmp80) cc_final: 0.8139 (mmp80)
REVERT: A  460 GLU cc_start: 0.8344 (pm20) cc_final: 0.8046 (pm20)
REVERT: A  724 LYS cc_start: 0.8831 (mmpt) cc_final: 0.8556 (mmpt)
REVERT: A  788 ASP cc_start: 0.8162 (t70) cc_final: 0.7768 (t0)
REVERT: A  834 GLU cc_start: 0.7485 (mp0) cc_final: 0.7171 (pm20)
REVERT: A  893 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8924 (mtpp)
REVERT: A 1124 ASP cc_start: 0.9085 (t70) cc_final: 0.8690 (t0)
REVERT: A 1225 MET cc_start: 0.8920 (mmt) cc_final: 0.8495 (mmt)
REVERT: A 1295 ARG cc_start: 0.8005 (mtt180) cc_final: 0.7550 (mtt180)
REVERT: A 1313 GLU cc_start: 0.8500 (tp30) cc_final: 0.8229 (mm-30)
REVERT: A 1440 ASP cc_start: 0.8308 (m-30) cc_final: 0.7968 (m-30)
REVERT: A 1442 GLU cc_start: 0.8186 (mp0) cc_final: 0.7883 (mp0)
REVERT: B  549 LYS cc_start: 0.8548 (tttm) cc_final: 0.8307 (tttt)
REVERT: B  554 ASP cc_start: 0.8674 (m-30) cc_final: 0.8328 (m-30)
REVERT: B  606 GLN cc_start: 0.8232 (mm-40) cc_final: 0.7827 (mm-40)
REVERT: B  669 ARG cc_start: 0.8443 (mtt-85) cc_final: 0.8013 (mmt90)
REVERT: B  695 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8155 (mp10)
REVERT: C  550 LEU cc_start: 0.8711 (mt) cc_final: 0.8465 (mt)
REVERT: C  554 ASP cc_start: 0.9144 (t0) cc_final: 0.8930 (m-30)
REVERT: C  564 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7988 (tp)
REVERT: C  577 MET cc_start: 0.8255 (tmm) cc_final: 0.7564 (tmt)
REVERT: D  555 ARG cc_start: 0.8723 (mpp80) cc_final: 0.8482 (mtp180)
REVERT: E  581 LYS cc_start: 0.8622 (tppt) cc_final: 0.8303 (mppt)
  outliers start: 18
  outliers final: 12
  residues processed: 247
  average time/residue: 0.6365
  time to fit residues: 170.2361
Evaluate side-chains
  249 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 235
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  381 MET
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 1218 VAL
Chi-restraints excluded: chain A residue 1222 LEU
Chi-restraints excluded: chain A residue 1231 THR
Chi-restraints excluded: chain B residue  597 VAL
Chi-restraints excluded: chain B residue  695 GLN
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 E residue  551 GLU
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 59 optimal weight:    9.9990
   chunk 109 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 105 optimal weight:    2.9990
   chunk 101 optimal weight:    0.4980
   chunk 159 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0970
   chunk 52 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.4382

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1074 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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.116219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.075579 restraints weight = 32166.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 3.55
r_work: 0.2762 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2764
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2764 r_free = 0.2764    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2764
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.2301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  13285  Z= 0.187
  Angle     :  0.664  15.321  17921  Z= 0.336
  Chirality :  0.044   0.180   2049
  Planarity :  0.004   0.063   2275
  Dihedral  :  4.266  22.543   1754
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 16.34 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.21), residues: 1604
  helix:  2.04 (0.18), residues: 911
  sheet:  0.04 (0.53), residues: 90
  loop :  0.17 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 202 
 TYR   0.014   0.001   TYR A 862 
 PHE   0.025   0.001   PHE A 726 
 TRP   0.013   0.001   TRP A 173 
 HIS   0.009   0.001   HIS E 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (13278)
  covalent geometry    : angle       0.66347 (17920)
  hydrogen bonds       : bond        0.04327 (  747)
  hydrogen bonds       : angle       4.44189 ( 2150)
  metal coordination   : bond        0.00860 (    7)
  metal coordination   : angle       1.62588 (    1)

********************** 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
  255 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 236
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 LYS cc_start: 0.9222 (mtmm) cc_final: 0.9002 (mppt)
REVERT: A  192 PHE cc_start: 0.8464 (m-80) cc_final: 0.7902 (m-80)
REVERT: A  193 ARG cc_start: 0.8407 (mmp80) cc_final: 0.8060 (mmp80)
REVERT: A  460 GLU cc_start: 0.8375 (pm20) cc_final: 0.8077 (pm20)
REVERT: A  724 LYS cc_start: 0.8845 (mmpt) cc_final: 0.8541 (mmpt)
REVERT: A  788 ASP cc_start: 0.8204 (t70) cc_final: 0.7819 (t0)
REVERT: A  834 GLU cc_start: 0.7522 (mp0) cc_final: 0.7199 (pm20)
REVERT: A 1099 ASP cc_start: 0.8975 (m-30) cc_final: 0.8717 (m-30)
REVERT: A 1124 ASP cc_start: 0.9077 (t70) cc_final: 0.8681 (t0)
REVERT: A 1225 MET cc_start: 0.8892 (mmt) cc_final: 0.8447 (mmt)
REVERT: A 1295 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7739 (mtt90)
REVERT: A 1313 GLU cc_start: 0.8507 (tp30) cc_final: 0.8237 (mm-30)
REVERT: A 1442 GLU cc_start: 0.8179 (mp0) cc_final: 0.7854 (mp0)
REVERT: B  549 LYS cc_start: 0.8525 (tttm) cc_final: 0.8253 (tttt)
REVERT: B  554 ASP cc_start: 0.8695 (m-30) cc_final: 0.8350 (m-30)
REVERT: B  606 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7807 (mm-40)
REVERT: B  695 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8142 (mp10)
REVERT: C  550 LEU cc_start: 0.8715 (mt) cc_final: 0.8503 (mt)
REVERT: C  564 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7959 (tp)
REVERT: C  577 MET cc_start: 0.8230 (tmm) cc_final: 0.7520 (tmt)
REVERT: E  581 LYS cc_start: 0.8657 (tppt) cc_final: 0.8273 (mppt)
  outliers start: 19
  outliers final: 14
  residues processed: 242
  average time/residue: 0.6499
  time to fit residues: 169.7106
Evaluate side-chains
  251 residues out of total 1465 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 235
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ILE
Chi-restraints excluded: chain A residue  348 ASP
Chi-restraints excluded: chain A residue  388 GLU
Chi-restraints excluded: chain A residue  716 SER
Chi-restraints excluded: chain A residue  723 LEU
Chi-restraints excluded: chain A residue  823 THR
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 B residue  597 VAL
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 E residue  551 GLU
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 160
   random chunks:
   chunk 83 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 102 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 71 optimal weight:    9.9990
   chunk 117 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1074 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 = 0.3616 r_free = 0.3616 target = 0.117765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.076595 restraints weight = 39185.171|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 3.92
r_work: 0.2768 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    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 = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.065         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2280

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= 0.149
  Angle     :  0.659  15.086  17921  Z= 0.333
  Chirality :  0.043   0.194   2049
  Planarity :  0.004   0.062   2275
  Dihedral  :  4.245  22.687   1754
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 16.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.21), residues: 1604
  helix:  2.06 (0.18), residues: 911
  sheet:  0.04 (0.53), residues: 90
  loop :  0.20 (0.26), residues: 603

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 202 
 TYR   0.011   0.001   TYR A 862 
 PHE   0.022   0.001   PHE A 726 
 TRP   0.011   0.001   TRP A1248 
 HIS   0.009   0.001   HIS E 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (13278)
  covalent geometry    : angle       0.65871 (17920)
  hydrogen bonds       : bond        0.04163 (  747)
  hydrogen bonds       : angle       4.40798 ( 2150)
  metal coordination   : bond        0.00408 (    7)
  metal coordination   : angle       2.40137 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7199.91 seconds
wall clock time: 122 minutes 55.18 seconds (7375.18 seconds total)