Starting phenix.real_space_refine
on Thu Sep 18 01:37:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9iva_60923/09_2025/9iva_60923.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9iva_60923/09_2025/9iva_60923.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9iva_60923/09_2025/9iva_60923.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9iva_60923/09_2025/9iva_60923.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9iva_60923/09_2025/9iva_60923.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9iva_60923/09_2025/9iva_60923.map"
  }
  resolution = 2.52
  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=   0.001 sd=   0.052
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      83      5.16       5
     C    8227      2.51       5
     N    2222      2.21       5
     O    2410      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 12944
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 10269
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1275, 10260
          Classifications: {'peptide': 1275}
          Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1226}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 1275, 10260
          Classifications: {'peptide': 1275}
          Link IDs: {'PCIS': 1, 'PTRANS': 47, 'TRANS': 1226}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 10458
    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   8540  SG  CYS A1191      46.188  29.703  25.478  1.00110.13           S
  ATOM  10095  SG  CYS A1428      41.689  30.009  26.167  1.00135.27           S
  ATOM  10101  SG  CYS A1429      45.033  30.483  27.696  1.00128.61           S
  ATOM   8890  SG  CYS A1236      26.566  28.786  33.344  1.00101.48           S
  ATOM   8913  SG  CYS A1239      27.255  25.349  34.924  1.00101.22           S

  Time building chain proxies: 4.97, per 1000 atoms: 0.38
  Number of scatterers: 12944
  At special positions: 0
  Unit cell: (96.725, 109.5, 168.813, 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      83     16.00
     O    2410      8.00
     N    2222      7.00
     C    8227      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: 0.83
  Conformation dependent library (CDL) restraints added in 962.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2301 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A1191 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A1428 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A1429 "
      pdb="  ZN A2302 "
        pdb="ZN    ZN A2302 " - pdb=" NE2 HIS A1423 "
        pdb="ZN    ZN A2302 " - pdb=" ND1 HIS A1421 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A1239 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A1236 "
      Number of angles added : 1


  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3086

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 7 sheets defined
      61.6% alpha, 5.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.43
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 10
    Processing helix  chain 'A' and resid 22 through 33
      removed outlier: 3.866A  pdb=" N   LEU A  26 " --> pdb=" O   VAL A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 57
      removed outlier: 3.532A  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: 3.734A  pdb=" N   ILE A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   LYS A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   LYS A 124 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 155
    Processing helix  chain 'A' and resid 156 through 163
    Processing helix  chain 'A' and resid 166 through 189
      removed outlier: 3.632A  pdb=" N   LYS A 189 " --> pdb=" O   LYS A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 193
      removed outlier: 3.971A  pdb=" N   ARG A 193 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 190 through 193'
    Processing helix  chain 'A' and resid 231 through 255
    Processing helix  chain 'A' and resid 260 through 273
      removed outlier: 3.879A  pdb=" N   ARG A 264 " --> pdb=" O   PRO A 260 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   ASN A 266 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 280
      removed outlier: 4.415A  pdb=" N   VAL A 278 " --> pdb=" O   PRO A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 288
      removed outlier: 3.981A  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 304 through 308
    Processing helix  chain 'A' and resid 309 through 327
      removed outlier: 3.932A  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: 3.743A  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: 3.555A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   HIS A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 410
      removed outlier: 3.713A  pdb=" N   ARG A 410 " --> pdb=" O   GLY A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 435
    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 487
      removed outlier: 3.648A  pdb=" N   TRP A 483 " --> pdb=" O   LYS A 480 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   ASP A 484 " --> pdb=" O   ASP A 481 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   VAL A 486 " --> pdb=" O   TRP A 483 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   TYR A 487 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 511
      removed outlier: 3.574A  pdb=" N   ASN A 511 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 526
      removed outlier: 3.700A  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: 3.613A  pdb=" N   LYS A 580 " --> pdb=" O   LYS A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 730
    Processing helix  chain 'A' and resid 731 through 747
      removed outlier: 4.824A  pdb=" N   ILE A 737 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   PHE A 738 " --> pdb=" O   SER A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 760
      removed outlier: 3.774A  pdb=" N   LYS A 757 " --> pdb=" O   ASN A 753 " (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
    Processing helix  chain 'A' and resid 904 through 910
      removed outlier: 3.886A  pdb=" N   SER A 908 " --> pdb=" O   GLN A 904 " (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: 3.854A  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 1083
      removed outlier: 3.707A  pdb=" N   ASN A1083 " --> pdb=" O   THR A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1086 through 1091
      removed outlier: 4.587A  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 1124
    Processing helix  chain 'A' and resid 1126 through 1137
    Processing helix  chain 'A' and resid 1155 through 1179
      removed outlier: 5.453A  pdb=" N   ASP A1166 " --> pdb=" O   LEU A1162 " (cutoff:3.500A)
      removed outlier: 5.561A  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 1220 through 1224
    Processing helix  chain 'A' and resid 1236 through 1242
      removed outlier: 3.609A  pdb=" N   GLY A1242 " --> pdb=" O   ILE A1238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1292 through 1309
    Processing helix  chain 'A' and resid 1312 through 1324
      removed outlier: 3.999A  pdb=" N   GLN A1324 " --> pdb=" O   TYR A1320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1329 through 1337
    Processing helix  chain 'A' and resid 1391 through 1407
    Processing helix  chain 'B' and resid 526 through 542
    Processing helix  chain 'B' and resid 542 through 574
      removed outlier: 4.064A  pdb=" N   ILE B 546 " --> pdb=" O   GLU B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 609
      removed outlier: 3.536A  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 688
    Processing helix  chain 'B' and resid 690 through 707
      removed outlier: 3.730A  pdb=" N   ILE B 694 " --> pdb=" O   ASN B 690 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 526 through 541
    Processing helix  chain 'C' and resid 542 through 574
    Processing helix  chain 'D' and resid 526 through 541
    Processing helix  chain 'D' and resid 542 through 578
    Processing helix  chain 'E' and resid 526 through 541
    Processing helix  chain 'E' and resid 542 through 573
    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
      removed outlier: 8.539A  pdb=" N   MET E 575 " --> pdb=" O   LEU B 594 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   MET E 577 " --> pdb=" O   PRO B 596 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   ILE B 598 " --> pdb=" O   MET E 577 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 418 through 419
    Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 556
      removed outlier: 3.698A  pdb=" N   PHE A 553 " --> pdb=" O   SER A 540 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   VAL A 537 " --> pdb=" O   VAL A 763 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   TYR A 765 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 824 through 827
      removed outlier: 3.646A  pdb=" N   ARG A 824 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 888 through 891
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1225 through 1231

    740 hydrogen bonds defined for protein.
    2126 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: 2.19

  Time building geometry restraints manager: 1.16 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: 4220
        1.34 -     1.46: 2013
        1.46 -     1.58: 6802
        1.58 -     1.69: 0
        1.69 -     1.81: 138
  Bond restraints: 13173
  Sorted by residual:
  bond pdb=" CA  ILE B 543 "
       pdb=" C   ILE B 543 "
    ideal  model  delta    sigma   weight residual
    1.524  1.542 -0.017 1.05e-02 9.07e+03 2.68e+00
  bond pdb=" CA  ILE D 543 "
       pdb=" C   ILE D 543 "
    ideal  model  delta    sigma   weight residual
    1.520  1.533 -0.014 8.80e-03 1.29e+04 2.38e+00
  bond pdb=" C   ILE B 543 "
       pdb=" N   PRO B 544 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.25e-02 6.40e+03 2.37e+00
  bond pdb=" CG1 ILE B 536 "
       pdb=" CD1 ILE B 536 "
    ideal  model  delta    sigma   weight residual
    1.513  1.459  0.054 3.90e-02 6.57e+02 1.89e+00
  bond pdb=" CG  LEU A 242 "
       pdb=" CD1 LEU A 242 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.81e+00
  ... (remaining 13168 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 17555
        2.49 -     4.98: 190
        4.98 -     7.47: 31
        7.47 -     9.95: 3
        9.95 -    12.44: 1
  Bond angle restraints: 17780
  Sorted by residual:
  angle pdb=" C   ASP A1139 "
        pdb=" N   THR A1140 "
        pdb=" CA  THR A1140 "
      ideal   model   delta    sigma   weight residual
     120.38  126.92   -6.54 1.37e+00 5.33e-01 2.28e+01
  angle pdb=" C   ASP B 657 "
        pdb=" N   ASP B 658 "
        pdb=" CA  ASP B 658 "
      ideal   model   delta    sigma   weight residual
     121.54  129.82   -8.28 1.91e+00 2.74e-01 1.88e+01
  angle pdb=" N   GLY A1148 "
        pdb=" CA  GLY A1148 "
        pdb=" C   GLY A1148 "
      ideal   model   delta    sigma   weight residual
     113.99  119.04   -5.05 1.28e+00 6.10e-01 1.56e+01
  angle pdb=" CA  SER A1152 "
        pdb=" C   SER A1152 "
        pdb=" N   GLY A1153 "
      ideal   model   delta    sigma   weight residual
     117.79  113.19    4.60 1.22e+00 6.72e-01 1.42e+01
  angle pdb=" N   ILE B 543 "
        pdb=" CA  ILE B 543 "
        pdb=" C   ILE B 543 "
      ideal   model   delta    sigma   weight residual
     108.88  116.88   -8.00 2.16e+00 2.14e-01 1.37e+01
  ... (remaining 17775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.10: 7296
       16.10 -    32.20: 645
       32.20 -    48.30: 150
       48.30 -    64.39: 18
       64.39 -    80.49: 9
  Dihedral angle restraints: 8118
    sinusoidal: 3376
      harmonic: 4742
  Sorted by residual:
  dihedral pdb=" CA  ARG B 634 "
           pdb=" C   ARG B 634 "
           pdb=" N   GLU B 635 "
           pdb=" CA  GLU B 635 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.24  -16.76     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  ARG A 551 "
           pdb=" C   ARG A 551 "
           pdb=" N   LEU A 552 "
           pdb=" CA  LEU A 552 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.53  -16.47     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  THR A 880 "
           pdb=" C   THR A 880 "
           pdb=" N   GLU A 881 "
           pdb=" CA  GLU A 881 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.70   16.30     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 8115 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1469
       0.046 -    0.092: 438
       0.092 -    0.138: 115
       0.138 -    0.184: 7
       0.184 -    0.229: 3
  Chirality restraints: 2032
  Sorted by residual:
  chirality pdb=" CB  THR A1291 "
            pdb=" CA  THR A1291 "
            pdb=" OG1 THR A1291 "
            pdb=" CG2 THR A1291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  GLU A 291 "
            pdb=" N   GLU A 291 "
            pdb=" C   GLU A 291 "
            pdb=" CB  GLU A 291 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  ASP B 658 "
            pdb=" N   ASP B 658 "
            pdb=" C   ASP B 658 "
            pdb=" CB  ASP B 658 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.57e-01
  ... (remaining 2029 not shown)

  Planarity restraints: 2258
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1084 "    0.042 5.00e-02 4.00e+02   6.37e-02 6.50e+00
        pdb=" N   PRO A1085 "   -0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO A1085 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A1085 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A1155 "    0.036 5.00e-02 4.00e+02   5.57e-02 4.96e+00
        pdb=" N   PRO A1156 "   -0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A1156 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A1156 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A  88 "   -0.033 5.00e-02 4.00e+02   5.02e-02 4.03e+00
        pdb=" N   PRO A  89 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A  89 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A  89 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 2255 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.00: 6284
        3.00 -     3.48: 13925
        3.48 -     3.95: 21714
        3.95 -     4.43: 25142
        4.43 -     4.90: 39746
  Nonbonded interactions: 106811
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A1223 "
            pdb="ZN    ZN A2301 "
     model   vdw
     2.529 2.230
  nonbonded pdb=" N   ASN A 211 "
            pdb=" O   ASN A 211 "
     model   vdw
     2.531 2.496
  nonbonded pdb=" N   ILE A 789 "
            pdb=" N   PHE A 790 "
     model   vdw
     2.572 2.560
  nonbonded pdb=" O   ASN A 929 "
            pdb=" ND2 ASN A 929 "
     model   vdw
     2.578 3.120
  nonbonded pdb=" N   SER A1152 "
            pdb=" N   GLY A1153 "
     model   vdw
     2.613 2.560
  ... (remaining 106806 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=0.49 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  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:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.720
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  13180  Z= 0.167
  Angle     :  0.670  12.443  17781  Z= 0.358
  Chirality :  0.046   0.229   2032
  Planarity :  0.005   0.064   2258
  Dihedral  : 13.055  80.493   5032
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  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:  0.41 (0.20), residues: 1591
  helix:  0.94 (0.17), residues: 902
  sheet: -0.06 (0.58), residues: 80
  loop : -0.59 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1117 
 TYR   0.012   0.002   TYR A 284 
 PHE   0.019   0.002   PHE A 399 
 TRP   0.009   0.001   TRP A1248 
 HIS   0.005   0.001   HIS C 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (13173)
  covalent geometry    : angle       0.66979 (17780)
  hydrogen bonds       : bond        0.13647 (  740)
  hydrogen bonds       : angle       5.99664 ( 2126)
  metal coordination   : bond        0.00416 (    7)
  metal coordination   : angle       2.78952 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 0.490 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ARG cc_start: 0.8607 (ttm110) cc_final: 0.8404 (ttp80)
REVERT: A  168 GLU cc_start: 0.8378 (tp30) cc_final: 0.7966 (tp30)
REVERT: A  233 GLU cc_start: 0.8882 (mp0) cc_final: 0.8369 (mp0)
REVERT: A  321 GLN cc_start: 0.8496 (tp-100) cc_final: 0.8284 (tp-100)
REVERT: A  376 LYS cc_start: 0.8968 (ttmm) cc_final: 0.8704 (tppp)
REVERT: A  469 MET cc_start: 0.8935 (ptp) cc_final: 0.8716 (ptp)
REVERT: A  824 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7268 (mpt180)
REVERT: A 1028 ASP cc_start: 0.8400 (t70) cc_final: 0.8155 (t0)
REVERT: A 1032 MET cc_start: 0.8544 (mtm) cc_final: 0.8270 (mtp)
REVERT: B  607 SER cc_start: 0.8131 (m) cc_final: 0.7823 (p)
REVERT: B  665 LYS cc_start: 0.8481 (tttm) cc_final: 0.8200 (tttm)
REVERT: D  559 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8473 (mtpp)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.6741
  time to fit residues: 201.4511
Evaluate side-chains
  210 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    0.0980
   chunk 149 optimal weight:    0.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 845 ASN
A 876 ASN
** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 651 GLN
B 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.136714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.096254 restraints weight = 36582.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 3.66
r_work: 0.3194 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13180  Z= 0.132
  Angle     :  0.599   9.245  17781  Z= 0.306
  Chirality :  0.042   0.166   2032
  Planarity :  0.005   0.060   2258
  Dihedral  :  4.126  15.907   1741
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.67 %
    Favored  : 86.48 %
  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:  1.33 (0.21), residues: 1591
  helix:  1.75 (0.17), residues: 899
  sheet: -0.35 (0.53), residues: 91
  loop : -0.17 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 202 
 TYR   0.018   0.001   TYR A1416 
 PHE   0.016   0.001   PHE A 399 
 TRP   0.014   0.001   TRP A1248 
 HIS   0.004   0.001   HIS C 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (13173)
  covalent geometry    : angle       0.59922 (17780)
  hydrogen bonds       : bond        0.03979 (  740)
  hydrogen bonds       : angle       4.61617 ( 2126)
  metal coordination   : bond        0.00360 (    7)
  metal coordination   : angle       2.32408 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 225
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ARG cc_start: 0.8495 (ttm110) cc_final: 0.8213 (ttp80)
REVERT: A  168 GLU cc_start: 0.8411 (tp30) cc_final: 0.7787 (tp30)
REVERT: A  233 GLU cc_start: 0.8900 (mp0) cc_final: 0.8279 (mp0)
REVERT: A  289 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7754 (mtm)
REVERT: A  321 GLN cc_start: 0.8397 (tp-100) cc_final: 0.8130 (tp-100)
REVERT: A  376 LYS cc_start: 0.8823 (ttmm) cc_final: 0.8527 (tppp)
REVERT: A  436 GLU cc_start: 0.7598 (mp0) cc_final: 0.7269 (mp0)
REVERT: A  472 LYS cc_start: 0.8425 (mmpt) cc_final: 0.8099 (mmpt)
REVERT: A  824 ARG cc_start: 0.7933 (mtp-110) cc_final: 0.7043 (mpt180)
REVERT: A  881 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.6508 (mp0)
REVERT: A  909 MET cc_start: 0.8824 (mmm) cc_final: 0.8498 (mmm)
REVERT: A 1028 ASP cc_start: 0.8351 (t70) cc_final: 0.8093 (t0)
REVERT: A 1237 GLN cc_start: 0.7738 (mt0) cc_final: 0.7192 (mt0)
REVERT: A 1295 ARG cc_start: 0.8066 (ptp-110) cc_final: 0.7858 (ptp-110)
REVERT: B  595 LYS cc_start: 0.7325 (OUTLIER) cc_final: 0.6962 (mtmm)
REVERT: B  607 SER cc_start: 0.7000 (m) cc_final: 0.6784 (p)
REVERT: B  678 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7982 (ttm170)
REVERT: B  686 ASN cc_start: 0.8519 (m110) cc_final: 0.8149 (m110)
REVERT: C  577 MET cc_start: 0.7356 (tmt) cc_final: 0.7054 (tmt)
REVERT: D  551 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8257 (tm-30)
REVERT: D  555 ARG cc_start: 0.8836 (mmm160) cc_final: 0.8335 (mtm110)
REVERT: E  581 LYS cc_start: 0.8756 (mppt) cc_final: 0.8504 (mppt)
  outliers start: 27
  outliers final: 5
  residues processed: 234
  average time/residue: 0.6984
  time to fit residues: 176.0644
Evaluate side-chains
  219 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 210
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue  595 LYS
Chi-restraints excluded: chain B residue  678 ARG
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain C residue  575 MET
Chi-restraints excluded: chain D residue  562 THR
Chi-restraints excluded: chain E residue  565 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 132 optimal weight:    1.9990
   chunk 148 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 83 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 105 optimal weight:    4.9990
   chunk 136 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
A 135 ASN
A 845 ASN
B 651 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.133483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.094223 restraints weight = 24578.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 3.00
r_work: 0.3170 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  13180  Z= 0.185
  Angle     :  0.627  11.714  17781  Z= 0.320
  Chirality :  0.044   0.172   2032
  Planarity :  0.005   0.046   2258
  Dihedral  :  4.147  16.599   1741
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.76 %
    Favored  : 83.53 %
  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:  1.32 (0.21), residues: 1591
  helix:  1.72 (0.17), residues: 905
  sheet: -0.59 (0.50), residues: 96
  loop : -0.11 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  36 
 TYR   0.018   0.002   TYR A  32 
 PHE   0.021   0.002   PHE A 553 
 TRP   0.014   0.002   TRP A1306 
 HIS   0.006   0.001   HIS C 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (13173)
  covalent geometry    : angle       0.62698 (17780)
  hydrogen bonds       : bond        0.04226 (  740)
  hydrogen bonds       : angle       4.50746 ( 2126)
  metal coordination   : bond        0.00534 (    7)
  metal coordination   : angle       2.00696 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 227
  time to evaluate  : 0.475 
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  152 ARG cc_start: 0.8514 (ttm110) cc_final: 0.8196 (ttp80)
REVERT: A  168 GLU cc_start: 0.8365 (tp30) cc_final: 0.7705 (tp30)
REVERT: A  233 GLU cc_start: 0.8900 (mp0) cc_final: 0.8246 (mp0)
REVERT: A  321 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8149 (tp-100)
REVERT: A  376 LYS cc_start: 0.8742 (ttmm) cc_final: 0.8509 (tppp)
REVERT: A  436 GLU cc_start: 0.7581 (mp0) cc_final: 0.7225 (mp0)
REVERT: A  471 MET cc_start: 0.7978 (mmp) cc_final: 0.7657 (mmp)
REVERT: A  472 LYS cc_start: 0.8542 (mmpt) cc_final: 0.8106 (mmpt)
REVERT: A  507 ASP cc_start: 0.7198 (t70) cc_final: 0.6923 (OUTLIER)
REVERT: A  824 ARG cc_start: 0.7865 (mtp-110) cc_final: 0.7007 (mpt180)
REVERT: A  881 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6568 (mp0)
REVERT: A  909 MET cc_start: 0.8870 (mmm) cc_final: 0.8531 (mmm)
REVERT: A 1028 ASP cc_start: 0.8299 (t70) cc_final: 0.8056 (t0)
REVERT: A 1306 TRP cc_start: 0.8282 (m100) cc_final: 0.8044 (m100)
REVERT: B  595 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.7124 (mtmm)
REVERT: B  607 SER cc_start: 0.7018 (m) cc_final: 0.6751 (p)
REVERT: B  669 ARG cc_start: 0.7924 (mtt-85) cc_final: 0.7724 (mtt-85)
REVERT: C  577 MET cc_start: 0.7392 (tmt) cc_final: 0.6905 (tmt)
REVERT: E  581 LYS cc_start: 0.8720 (mppt) cc_final: 0.8438 (mppt)
  outliers start: 25
  outliers final: 4
  residues processed: 238
  average time/residue: 0.7333
  time to fit residues: 187.8177
Evaluate side-chains
  220 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 215
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain B residue  595 LYS
Chi-restraints excluded: chain C residue  537 GLU
Chi-restraints excluded: chain E residue  565 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 107 optimal weight:    0.4980
   chunk 70 optimal weight:    0.0870
   chunk 121 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 59 optimal weight:    0.3980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 131 ASN
A 845 ASN
B 651 GLN
B 695 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.135794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.095204 restraints weight = 36611.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 3.66
r_work: 0.3168 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3223
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3223 r_free = 0.3223    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3223
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13180  Z= 0.120
  Angle     :  0.584   9.500  17781  Z= 0.295
  Chirality :  0.041   0.160   2032
  Planarity :  0.004   0.047   2258
  Dihedral  :  3.982  16.284   1741
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 15.92 %
    Favored  : 83.05 %
  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:  1.59 (0.21), residues: 1591
  helix:  1.97 (0.17), residues: 901
  sheet: -0.54 (0.51), residues: 96
  loop : -0.03 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D 555 
 TYR   0.011   0.001   TYR A 793 
 PHE   0.016   0.001   PHE A 399 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.003   0.001   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (13173)
  covalent geometry    : angle       0.58379 (17780)
  hydrogen bonds       : bond        0.03638 (  740)
  hydrogen bonds       : angle       4.30468 ( 2126)
  metal coordination   : bond        0.00273 (    7)
  metal coordination   : angle       2.03458 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 224
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8082 (mmmt) cc_final: 0.7719 (mmtm)
REVERT: A  141 ARG cc_start: 0.7747 (ptm-80) cc_final: 0.7497 (ppt90)
REVERT: A  152 ARG cc_start: 0.8528 (ttm110) cc_final: 0.8245 (ttp80)
REVERT: A  168 GLU cc_start: 0.8396 (tp30) cc_final: 0.7756 (tp30)
REVERT: A  193 ARG cc_start: 0.7065 (mmt90) cc_final: 0.6850 (mmt90)
REVERT: A  233 GLU cc_start: 0.8929 (mp0) cc_final: 0.8281 (mp0)
REVERT: A  291 GLU cc_start: 0.8108 (pm20) cc_final: 0.7898 (mp0)
REVERT: A  321 GLN cc_start: 0.8404 (tp-100) cc_final: 0.8155 (tp-100)
REVERT: A  376 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8614 (tppp)
REVERT: A  436 GLU cc_start: 0.7639 (mp0) cc_final: 0.7233 (mp0)
REVERT: A  471 MET cc_start: 0.8013 (mmp) cc_final: 0.7608 (mmp)
REVERT: A  472 LYS cc_start: 0.8535 (mmpt) cc_final: 0.8102 (mmpt)
REVERT: A  507 ASP cc_start: 0.7232 (t70) cc_final: 0.6946 (OUTLIER)
REVERT: A  743 ASP cc_start: 0.7292 (m-30) cc_final: 0.7082 (m-30)
REVERT: A  824 ARG cc_start: 0.7891 (mtp-110) cc_final: 0.6993 (mpt180)
REVERT: A  881 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.6560 (mp0)
REVERT: A 1028 ASP cc_start: 0.8362 (t70) cc_final: 0.8122 (t0)
REVERT: A 1225 MET cc_start: 0.8376 (mtp) cc_final: 0.7965 (mmm)
REVERT: A 1295 ARG cc_start: 0.8053 (ptp-110) cc_final: 0.7790 (ptp-110)
REVERT: A 1306 TRP cc_start: 0.8330 (m100) cc_final: 0.8115 (m100)
REVERT: B  607 SER cc_start: 0.6946 (m) cc_final: 0.6677 (p)
REVERT: B  645 GLU cc_start: 0.8159 (mp0) cc_final: 0.7406 (pm20)
REVERT: B  658 ASP cc_start: 0.7982 (p0) cc_final: 0.7758 (p0)
REVERT: B  669 ARG cc_start: 0.7935 (mtt-85) cc_final: 0.7735 (mtt-85)
REVERT: B  686 ASN cc_start: 0.8491 (m110) cc_final: 0.8074 (m110)
REVERT: B  690 ASN cc_start: 0.8483 (p0) cc_final: 0.8221 (p0)
REVERT: B  695 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8564 (mp10)
REVERT: C  577 MET cc_start: 0.7422 (tmt) cc_final: 0.6840 (tmt)
REVERT: D  551 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8281 (tm-30)
REVERT: D  555 ARG cc_start: 0.8977 (mmm160) cc_final: 0.8314 (mtm110)
REVERT: E  581 LYS cc_start: 0.8692 (mppt) cc_final: 0.8322 (mppt)
  outliers start: 15
  outliers final: 3
  residues processed: 230
  average time/residue: 0.7388
  time to fit residues: 182.9638
Evaluate side-chains
  215 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 212
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain A residue  919 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 116 optimal weight:    7.9990
   chunk 152 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 108 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 126 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
A 845 ASN
A 876 ASN
B 651 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.132009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.092435 restraints weight = 28279.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 3.19
r_work: 0.3137 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3183
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3183 r_free = 0.3183    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3183
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  13180  Z= 0.207
  Angle     :  0.643  12.057  17781  Z= 0.324
  Chirality :  0.044   0.160   2032
  Planarity :  0.005   0.059   2258
  Dihedral  :  4.159  16.904   1741
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 15.51 %
    Favored  : 82.70 %
  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:  1.44 (0.21), residues: 1591
  helix:  1.84 (0.17), residues: 905
  sheet: -0.57 (0.51), residues: 96
  loop : -0.09 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A 202 
 TYR   0.018   0.002   TYR A  32 
 PHE   0.025   0.002   PHE A 553 
 TRP   0.013   0.002   TRP A1248 
 HIS   0.005   0.001   HIS C 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 (13173)
  covalent geometry    : angle       0.64299 (17780)
  hydrogen bonds       : bond        0.04223 (  740)
  hydrogen bonds       : angle       4.42110 ( 2126)
  metal coordination   : bond        0.00992 (    7)
  metal coordination   : angle       0.14411 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 222
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7759 (mmtm)
REVERT: A  141 ARG cc_start: 0.7833 (ptm-80) cc_final: 0.7570 (ppt90)
REVERT: A  152 ARG cc_start: 0.8540 (ttm110) cc_final: 0.8226 (ttp80)
REVERT: A  168 GLU cc_start: 0.8426 (tp30) cc_final: 0.7722 (tp30)
REVERT: A  233 GLU cc_start: 0.8939 (mp0) cc_final: 0.8280 (mp0)
REVERT: A  376 LYS cc_start: 0.8755 (ttmm) cc_final: 0.8533 (tppp)
REVERT: A  436 GLU cc_start: 0.7647 (mp0) cc_final: 0.7232 (mp0)
REVERT: A  471 MET cc_start: 0.8094 (OUTLIER) cc_final: 0.7772 (mmp)
REVERT: A  472 LYS cc_start: 0.8617 (mmpt) cc_final: 0.8286 (mmmt)
REVERT: A  507 ASP cc_start: 0.7269 (t70) cc_final: 0.7039 (t0)
REVERT: A  824 ARG cc_start: 0.7848 (mtp-110) cc_final: 0.6966 (mpt180)
REVERT: A  881 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.6679 (mp0)
REVERT: A  909 MET cc_start: 0.8854 (mmm) cc_final: 0.8521 (mmm)
REVERT: A 1028 ASP cc_start: 0.8325 (t70) cc_final: 0.8092 (t0)
REVERT: A 1074 ASN cc_start: 0.7407 (m-40) cc_final: 0.7163 (m-40)
REVERT: A 1306 TRP cc_start: 0.8397 (m100) cc_final: 0.8190 (m100)
REVERT: B  607 SER cc_start: 0.7054 (m) cc_final: 0.6752 (p)
REVERT: B  658 ASP cc_start: 0.7946 (p0) cc_final: 0.7725 (p0)
REVERT: B  669 ARG cc_start: 0.7988 (mtt-85) cc_final: 0.7772 (mtt-85)
REVERT: B  686 ASN cc_start: 0.8507 (m110) cc_final: 0.8104 (m110)
REVERT: B  690 ASN cc_start: 0.8465 (p0) cc_final: 0.7683 (p0)
REVERT: B  692 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8176 (mp0)
REVERT: B  695 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8588 (mp10)
REVERT: C  577 MET cc_start: 0.7378 (tmt) cc_final: 0.6841 (tmt)
REVERT: E  581 LYS cc_start: 0.8670 (mppt) cc_final: 0.8312 (mppt)
  outliers start: 24
  outliers final: 6
  residues processed: 233
  average time/residue: 0.7188
  time to fit residues: 180.5230
Evaluate side-chains
  222 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 214
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  471 MET
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue  536 ILE
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain E residue  535 HIS
Chi-restraints excluded: chain E residue  546 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 82 optimal weight:    0.6980
   chunk 115 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 83 optimal weight:    0.5980
   chunk 152 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 146 optimal weight:    0.8980
   chunk 68 optimal weight:    0.9990
   chunk 158 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0870
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 321 GLN
A 845 ASN
B 651 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.135109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.096216 restraints weight = 24280.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.98
r_work: 0.3204 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3249
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3249 r_free = 0.3249    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3249
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  13180  Z= 0.124
  Angle     :  0.607  12.286  17781  Z= 0.304
  Chirality :  0.042   0.168   2032
  Planarity :  0.004   0.062   2258
  Dihedral  :  4.003  16.711   1741
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 16.82 %
    Favored  : 81.74 %
  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:  1.68 (0.22), residues: 1591
  helix:  2.05 (0.18), residues: 901
  sheet: -0.49 (0.51), residues: 96
  loop :  0.00 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 202 
 TYR   0.010   0.001   TYR A 284 
 PHE   0.016   0.001   PHE A 399 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.003   0.001   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (13173)
  covalent geometry    : angle       0.60727 (17780)
  hydrogen bonds       : bond        0.03655 (  740)
  hydrogen bonds       : angle       4.28711 ( 2126)
  metal coordination   : bond        0.00272 (    7)
  metal coordination   : angle       1.64005 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 219
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8114 (mmmt) cc_final: 0.7761 (mmtm)
REVERT: A  141 ARG cc_start: 0.7738 (ptm-80) cc_final: 0.7524 (ppt90)
REVERT: A  152 ARG cc_start: 0.8546 (ttm110) cc_final: 0.8295 (ttp80)
REVERT: A  168 GLU cc_start: 0.8354 (tp30) cc_final: 0.7700 (tp30)
REVERT: A  233 GLU cc_start: 0.8942 (mp0) cc_final: 0.8346 (mp0)
REVERT: A  376 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8556 (tppp)
REVERT: A  436 GLU cc_start: 0.7608 (mp0) cc_final: 0.7231 (mp0)
REVERT: A  471 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7497 (mmp)
REVERT: A  472 LYS cc_start: 0.8572 (mmpt) cc_final: 0.8158 (mmpt)
REVERT: A  507 ASP cc_start: 0.7280 (t70) cc_final: 0.7038 (OUTLIER)
REVERT: A  824 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.6951 (mpt180)
REVERT: A 1028 ASP cc_start: 0.8309 (t70) cc_final: 0.8080 (t0)
REVERT: A 1074 ASN cc_start: 0.7435 (m-40) cc_final: 0.7189 (m-40)
REVERT: A 1225 MET cc_start: 0.8231 (mtp) cc_final: 0.7914 (mmm)
REVERT: A 1306 TRP cc_start: 0.8364 (m100) cc_final: 0.8141 (m100)
REVERT: A 1324 GLN cc_start: 0.7677 (pm20) cc_final: 0.7232 (mp10)
REVERT: B  607 SER cc_start: 0.7021 (m) cc_final: 0.6717 (p)
REVERT: B  645 GLU cc_start: 0.8138 (mp0) cc_final: 0.7351 (pm20)
REVERT: B  669 ARG cc_start: 0.7958 (mtt-85) cc_final: 0.7754 (mtt-85)
REVERT: B  686 ASN cc_start: 0.8505 (m110) cc_final: 0.8138 (m110)
REVERT: B  695 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8623 (mp10)
REVERT: C  577 MET cc_start: 0.7394 (tmt) cc_final: 0.6798 (tmt)
REVERT: E  549 LYS cc_start: 0.8173 (ptmm) cc_final: 0.7927 (ptmt)
REVERT: E  581 LYS cc_start: 0.8670 (mppt) cc_final: 0.8379 (mppt)
  outliers start: 19
  outliers final: 9
  residues processed: 229
  average time/residue: 0.6922
  time to fit residues: 170.7722
Evaluate side-chains
  218 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 209
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  471 MET
Chi-restraints excluded: chain A residue  880 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue 1411 LEU
Chi-restraints excluded: chain B residue  536 ILE
Chi-restraints excluded: chain C residue  575 MET
Chi-restraints excluded: chain E residue  535 HIS
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 101 optimal weight:    0.9980
   chunk 71 optimal weight:    0.4980
   chunk 74 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 148 optimal weight:   20.0000
   chunk 123 optimal weight:    0.2980
   chunk 132 optimal weight:    0.0870
   chunk 110 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 845 ASN
A 876 ASN
B 651 GLN
B 690 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.135766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.095085 restraints weight = 38286.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 3.68
r_work: 0.3186 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13180  Z= 0.121
  Angle     :  0.612  13.279  17781  Z= 0.306
  Chirality :  0.042   0.170   2032
  Planarity :  0.004   0.056   2258
  Dihedral  :  3.922  16.076   1741
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 16.27 %
    Favored  : 82.02 %
  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:  1.73 (0.22), residues: 1591
  helix:  2.03 (0.17), residues: 910
  sheet: -0.33 (0.52), residues: 96
  loop :  0.09 (0.27), residues: 585

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A1180 
 TYR   0.010   0.001   TYR A 284 
 PHE   0.026   0.001   PHE A 553 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.002   0.001   HIS A 314 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (13173)
  covalent geometry    : angle       0.61166 (17780)
  hydrogen bonds       : bond        0.03542 (  740)
  hydrogen bonds       : angle       4.28865 ( 2126)
  metal coordination   : bond        0.00273 (    7)
  metal coordination   : angle       1.54253 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 214
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7781 (mmtm)
REVERT: A  141 ARG cc_start: 0.7758 (ptm-80) cc_final: 0.7503 (ppt90)
REVERT: A  152 ARG cc_start: 0.8548 (ttm110) cc_final: 0.8299 (ttp80)
REVERT: A  168 GLU cc_start: 0.8382 (tp30) cc_final: 0.7696 (tp30)
REVERT: A  233 GLU cc_start: 0.8951 (mp0) cc_final: 0.8390 (mp0)
REVERT: A  321 GLN cc_start: 0.8504 (tp40) cc_final: 0.8252 (tp-100)
REVERT: A  376 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8522 (tppp)
REVERT: A  379 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8223 (pp20)
REVERT: A  436 GLU cc_start: 0.7628 (mp0) cc_final: 0.7229 (mp0)
REVERT: A  824 ARG cc_start: 0.7873 (mtp-110) cc_final: 0.6962 (mpt180)
REVERT: A  881 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6729 (mp0)
REVERT: A  909 MET cc_start: 0.8875 (mmm) cc_final: 0.8619 (mmm)
REVERT: A 1028 ASP cc_start: 0.8336 (t70) cc_final: 0.8108 (t0)
REVERT: A 1074 ASN cc_start: 0.7401 (m-40) cc_final: 0.7154 (m-40)
REVERT: A 1225 MET cc_start: 0.8202 (mtp) cc_final: 0.7930 (mmm)
REVERT: A 1306 TRP cc_start: 0.8381 (m100) cc_final: 0.8168 (m100)
REVERT: B  607 SER cc_start: 0.6998 (m) cc_final: 0.6706 (p)
REVERT: B  645 GLU cc_start: 0.8110 (mp0) cc_final: 0.7325 (pm20)
REVERT: B  695 GLN cc_start: 0.8848 (mm-40) cc_final: 0.8642 (mp10)
REVERT: C  577 MET cc_start: 0.7401 (tmt) cc_final: 0.6778 (tmt)
REVERT: E  549 LYS cc_start: 0.8146 (ptmm) cc_final: 0.7862 (ptmt)
REVERT: E  559 LYS cc_start: 0.8468 (tmmt) cc_final: 0.8188 (pptt)
REVERT: E  581 LYS cc_start: 0.8691 (mppt) cc_final: 0.8372 (mppt)
  outliers start: 23
  outliers final: 7
  residues processed: 225
  average time/residue: 0.6645
  time to fit residues: 161.5424
Evaluate side-chains
  215 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 206
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  880 THR
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue 1411 LEU
Chi-restraints excluded: chain C residue  575 MET
Chi-restraints excluded: chain E residue  535 HIS
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 50 optimal weight:    4.9990
   chunk 96 optimal weight:    8.9990
   chunk 28 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 148 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 115 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 845 ASN
** A1324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 651 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.135181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.095777 restraints weight = 24217.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.99
r_work: 0.3212 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3264
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3264 r_free = 0.3264    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3264
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  13180  Z= 0.134
  Angle     :  0.635  14.357  17781  Z= 0.319
  Chirality :  0.042   0.153   2032
  Planarity :  0.004   0.059   2258
  Dihedral  :  3.929  15.826   1741
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 17.16 %
    Favored  : 81.61 %
  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:  1.71 (0.22), residues: 1591
  helix:  2.00 (0.18), residues: 906
  sheet: -0.29 (0.52), residues: 96
  loop :  0.09 (0.27), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A1180 
 TYR   0.010   0.001   TYR A 284 
 PHE   0.017   0.001   PHE A 399 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.002   0.001   HIS C 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (13173)
  covalent geometry    : angle       0.63529 (17780)
  hydrogen bonds       : bond        0.03654 (  740)
  hydrogen bonds       : angle       4.34193 ( 2126)
  metal coordination   : bond        0.00359 (    7)
  metal coordination   : angle       1.25557 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 214
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7794 (mmtm)
REVERT: A  141 ARG cc_start: 0.7718 (ptm-80) cc_final: 0.7473 (ppt90)
REVERT: A  152 ARG cc_start: 0.8530 (ttm110) cc_final: 0.8290 (ttp80)
REVERT: A  168 GLU cc_start: 0.8342 (tp30) cc_final: 0.7673 (tp30)
REVERT: A  233 GLU cc_start: 0.8935 (mp0) cc_final: 0.8309 (mp0)
REVERT: A  376 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8433 (tppp)
REVERT: A  379 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8156 (pp20)
REVERT: A  436 GLU cc_start: 0.7635 (mp0) cc_final: 0.7251 (mp0)
REVERT: A  824 ARG cc_start: 0.7860 (mtp-110) cc_final: 0.6980 (mpt180)
REVERT: A  881 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.6713 (mp0)
REVERT: A  909 MET cc_start: 0.8887 (mmm) cc_final: 0.8633 (mmm)
REVERT: A 1028 ASP cc_start: 0.8296 (t70) cc_final: 0.8072 (t0)
REVERT: A 1225 MET cc_start: 0.8177 (mtp) cc_final: 0.7909 (mmm)
REVERT: A 1295 ARG cc_start: 0.8059 (ptp-110) cc_final: 0.7822 (ptp-110)
REVERT: A 1306 TRP cc_start: 0.8379 (m100) cc_final: 0.8160 (m100)
REVERT: B  607 SER cc_start: 0.7048 (m) cc_final: 0.6743 (p)
REVERT: B  645 GLU cc_start: 0.8143 (mp0) cc_final: 0.7367 (pm20)
REVERT: B  695 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8533 (mp10)
REVERT: C  577 MET cc_start: 0.7457 (tmt) cc_final: 0.6911 (tmt)
REVERT: E  559 LYS cc_start: 0.8485 (tmmt) cc_final: 0.8168 (pptt)
REVERT: E  581 LYS cc_start: 0.8681 (mppt) cc_final: 0.8387 (mppt)
  outliers start: 16
  outliers final: 8
  residues processed: 222
  average time/residue: 0.6869
  time to fit residues: 164.6666
Evaluate side-chains
  219 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 209
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  880 THR
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue 1411 LEU
Chi-restraints excluded: chain C residue  575 MET
Chi-restraints excluded: chain E residue  535 HIS
Chi-restraints excluded: chain E residue  546 ILE
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 67 optimal weight:    0.1980
   chunk 157 optimal weight:    0.9990
   chunk 120 optimal weight:   10.0000
   chunk 11 optimal weight:    0.1980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 29 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
A 845 ASN
A1324 GLN
B 651 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.134066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.092866 restraints weight = 39396.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 3.74
r_work: 0.3150 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3218
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3218 r_free = 0.3218    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3218
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  13180  Z= 0.155
  Angle     :  0.651  13.558  17781  Z= 0.327
  Chirality :  0.043   0.164   2032
  Planarity :  0.004   0.061   2258
  Dihedral  :  4.004  16.303   1741
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 17.16 %
    Favored  : 81.74 %
  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:  1.64 (0.22), residues: 1591
  helix:  1.94 (0.17), residues: 904
  sheet: -0.26 (0.52), residues: 96
  loop :  0.07 (0.26), residues: 591

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A1180 
 TYR   0.019   0.001   TYR A1316 
 PHE   0.025   0.001   PHE A 553 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.003   0.001   HIS C 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (13173)
  covalent geometry    : angle       0.65079 (17780)
  hydrogen bonds       : bond        0.03864 (  740)
  hydrogen bonds       : angle       4.38440 ( 2126)
  metal coordination   : bond        0.00535 (    7)
  metal coordination   : angle       0.76987 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 217
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8142 (mmmt) cc_final: 0.7814 (mmtm)
REVERT: A  141 ARG cc_start: 0.7784 (ptm-80) cc_final: 0.7533 (ppt90)
REVERT: A  152 ARG cc_start: 0.8547 (ttm110) cc_final: 0.8300 (ttp80)
REVERT: A  168 GLU cc_start: 0.8445 (tp30) cc_final: 0.7754 (tp30)
REVERT: A  233 GLU cc_start: 0.8977 (mp0) cc_final: 0.8372 (mp0)
REVERT: A  376 LYS cc_start: 0.8846 (ttmm) cc_final: 0.8467 (tppp)
REVERT: A  379 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8180 (pp20)
REVERT: A  436 GLU cc_start: 0.7674 (mp0) cc_final: 0.7262 (mp0)
REVERT: A  471 MET cc_start: 0.7631 (mmm) cc_final: 0.7099 (mmm)
REVERT: A  472 LYS cc_start: 0.8568 (mmpt) cc_final: 0.8168 (mmpt)
REVERT: A  824 ARG cc_start: 0.7911 (mtp-110) cc_final: 0.6979 (mpt180)
REVERT: A  881 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6759 (mp0)
REVERT: A  909 MET cc_start: 0.8896 (mmm) cc_final: 0.8632 (mmm)
REVERT: A 1028 ASP cc_start: 0.8347 (t70) cc_final: 0.8120 (t0)
REVERT: A 1074 ASN cc_start: 0.7421 (m-40) cc_final: 0.7193 (m-40)
REVERT: A 1225 MET cc_start: 0.8292 (mtp) cc_final: 0.7924 (mmm)
REVERT: A 1306 TRP cc_start: 0.8375 (m100) cc_final: 0.8127 (m100)
REVERT: A 1364 ASN cc_start: 0.8334 (t0) cc_final: 0.8031 (t0)
REVERT: B  607 SER cc_start: 0.7068 (m) cc_final: 0.6763 (p)
REVERT: B  645 GLU cc_start: 0.8144 (mp0) cc_final: 0.7383 (pm20)
REVERT: B  686 ASN cc_start: 0.8456 (m110) cc_final: 0.8024 (m110)
REVERT: B  695 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8440 (mp10)
REVERT: C  577 MET cc_start: 0.7467 (tmt) cc_final: 0.6906 (tmt)
REVERT: E  549 LYS cc_start: 0.8135 (ptmm) cc_final: 0.7873 (ptmm)
REVERT: E  581 LYS cc_start: 0.8653 (mppt) cc_final: 0.8286 (mppt)
  outliers start: 14
  outliers final: 9
  residues processed: 222
  average time/residue: 0.6863
  time to fit residues: 164.2967
Evaluate side-chains
  220 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 209
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  880 THR
Chi-restraints excluded: chain A residue  881 GLU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain C residue  574 MET
Chi-restraints excluded: chain C residue  575 MET
Chi-restraints excluded: chain E residue  535 HIS
Chi-restraints excluded: chain E residue  546 ILE
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 148 optimal weight:    6.9990
   chunk 125 optimal weight:    1.9990
   chunk 121 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 77 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0570
   chunk 52 optimal weight:    0.3980
   chunk 21 optimal weight:    0.5980
   chunk 110 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.5498

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
A 845 ASN
A 876 ASN
A1324 GLN
B 651 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.135504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.094568 restraints weight = 38162.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 3.72
r_work: 0.3181 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3247
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3247 r_free = 0.3247    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3247
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13180  Z= 0.129
  Angle     :  0.652  15.647  17781  Z= 0.327
  Chirality :  0.042   0.161   2032
  Planarity :  0.004   0.062   2258
  Dihedral  :  3.942  15.996   1741
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 17.91 %
    Favored  : 81.26 %
  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:  1.80 (0.22), residues: 1591
  helix:  2.04 (0.18), residues: 901
  sheet: -0.22 (0.52), residues: 96
  loop :  0.21 (0.27), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG B 555 
 TYR   0.016   0.001   TYR A1316 
 PHE   0.016   0.001   PHE A 399 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.003   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (13173)
  covalent geometry    : angle       0.65224 (17780)
  hydrogen bonds       : bond        0.03611 (  740)
  hydrogen bonds       : angle       4.33278 ( 2126)
  metal coordination   : bond        0.00257 (    7)
  metal coordination   : angle       1.74666 (    1)

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

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

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3182 Ramachandran restraints generated.
    1591 Oldfield, 0 Emsley, 1591 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 221
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  141 ARG cc_start: 0.7727 (ptm-80) cc_final: 0.7495 (ppt90)
REVERT: A  152 ARG cc_start: 0.8536 (ttm110) cc_final: 0.8295 (ttp80)
REVERT: A  168 GLU cc_start: 0.8401 (tp30) cc_final: 0.7704 (tp30)
REVERT: A  233 GLU cc_start: 0.8959 (mp0) cc_final: 0.8393 (mp0)
REVERT: A  376 LYS cc_start: 0.8817 (ttmm) cc_final: 0.8492 (tppp)
REVERT: A  379 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8196 (pp20)
REVERT: A  436 GLU cc_start: 0.7633 (mp0) cc_final: 0.7254 (mp0)
REVERT: A  824 ARG cc_start: 0.7886 (mtp-110) cc_final: 0.6945 (mpt180)
REVERT: A 1028 ASP cc_start: 0.8354 (t70) cc_final: 0.8126 (t0)
REVERT: A 1074 ASN cc_start: 0.7395 (m-40) cc_final: 0.7162 (m-40)
REVERT: A 1225 MET cc_start: 0.8158 (mtp) cc_final: 0.7938 (mmm)
REVERT: A 1306 TRP cc_start: 0.8312 (m100) cc_final: 0.8093 (m100)
REVERT: B  607 SER cc_start: 0.7020 (m) cc_final: 0.6719 (p)
REVERT: B  645 GLU cc_start: 0.8140 (mp0) cc_final: 0.7334 (pm20)
REVERT: B  686 ASN cc_start: 0.8454 (m110) cc_final: 0.8021 (m110)
REVERT: B  695 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8448 (mp10)
REVERT: C  577 MET cc_start: 0.7483 (tmt) cc_final: 0.6879 (tmt)
REVERT: E  581 LYS cc_start: 0.8641 (mppt) cc_final: 0.8309 (mppt)
  outliers start: 10
  outliers final: 8
  residues processed: 225
  average time/residue: 0.6509
  time to fit residues: 158.3588
Evaluate side-chains
  220 residues out of total 1453 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 211
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  379 GLU
Chi-restraints excluded: chain A residue  880 THR
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain C residue  575 MET
Chi-restraints excluded: chain D residue  576 ILE
Chi-restraints excluded: chain E residue  535 HIS
Chi-restraints excluded: chain E residue  546 ILE
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 120 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 154 optimal weight:    9.9990
   chunk 140 optimal weight:    0.1980
   chunk 93 optimal weight:    0.0980
   chunk 98 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
A 845 ASN
** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1324 GLN
B 651 GLN
B 690 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.135891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.095394 restraints weight = 33858.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 3.52
r_work: 0.3204 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13180  Z= 0.129
  Angle     :  0.638  13.359  17781  Z= 0.323
  Chirality :  0.042   0.159   2032
  Planarity :  0.005   0.062   2258
  Dihedral  :  3.931  16.042   1741
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 18.74 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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 (0.22), residues: 1591
  helix:  2.02 (0.18), residues: 900
  sheet: -0.05 (0.52), residues: 94
  loop :  0.24 (0.27), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 555 
 TYR   0.016   0.001   TYR A1316 
 PHE   0.025   0.001   PHE A 553 
 TRP   0.013   0.001   TRP A1248 
 HIS   0.002   0.001   HIS C 570 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (13173)
  covalent geometry    : angle       0.63800 (17780)
  hydrogen bonds       : bond        0.03638 (  740)
  hydrogen bonds       : angle       4.32032 ( 2126)
  metal coordination   : bond        0.00272 (    7)
  metal coordination   : angle       1.55576 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6494.43 seconds
wall clock time: 111 minutes 6.79 seconds (6666.79 seconds total)