Starting phenix.real_space_refine
on Wed Mar  4 02:35:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jpt_22422/03_2026/7jpt_22422.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jpt_22422/03_2026/7jpt_22422.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jpt_22422/03_2026/7jpt_22422.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jpt_22422/03_2026/7jpt_22422.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jpt_22422/03_2026/7jpt_22422.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jpt_22422/03_2026/7jpt_22422.map"
  }
  resolution = 3.2
  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=   0.015
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: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    6576      2.51       5
     N    1728      2.21       5
     O    1850      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10220
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 10153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1327, 10153
          Classifications: {'peptide': 1327}
          Incomplete info: {'truncation_to_alanine': 183}
          Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 62, 'TRANS': 1260}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 687
          Unresolved non-hydrogen angles: 865
          Unresolved non-hydrogen dihedrals: 547
          Unresolved non-hydrogen chiralities: 34
          Planarities with less than four sites: {'ASP:plan': 24, 'GLU:plan': 47, 'ARG:plan': 19, 'ASN:plan1': 13, 'GLN:plan1': 5, 'HIS:plan': 6, 'TYR:plan': 5, 'TRP:plan': 1, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 500
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 2.70, per 1000 atoms: 0.26
  Number of scatterers: 10220
  At special positions: 0
  Unit cell: (86.92, 99.64, 125.08, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    1850      8.00
     N    1728      7.00
     C    6576      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=23, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  46 " - pdb=" SG  CYS A  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  83 " - pdb=" SG  CYS A 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 110 " - pdb=" SG  CYS A 150 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 169 " - pdb=" SG  CYS A 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 183 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 216 " - pdb=" SG  CYS A 229 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 247 " - pdb=" SG  CYS A 340 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 317 " - pdb=" SG  CYS A 332 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 361 " - pdb=" SG  CYS A 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 389 " - pdb=" SG  CYS A 485 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 462 " - pdb=" SG  CYS A 477 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 501 " - pdb=" SG  CYS A 514 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 528 " - pdb=" SG  CYS A 623 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 597 " - pdb=" SG  CYS A 614 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 678 " - pdb=" SG  CYS A 782 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 840 " - pdb=" SG  CYS A 930 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 904 " - pdb=" SG  CYS A 922 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 980 " - pdb=" SG  CYS A1089 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1060 " - pdb=" SG  CYS A1080 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1131 " - pdb=" SG  CYS A1220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1197 " - pdb=" SG  CYS A1211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1239 " - pdb=" SG  CYS A1255 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1277 " - pdb=" SG  CYS A1380 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG A1801 " - " ASN A1253 "
      " NAG B   1 " - " ASN A1076 "
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 591.1 milliseconds
  

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2508

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 28 sheets defined
      19.0% alpha, 17.3% 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 61 through 65
      removed outlier: 4.017A  pdb=" N   ASP A  64 " --> pdb=" O   GLU A  61 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 73
      No H-bonds generated for 'chain 'A' and resid 71 through 73'
    Processing helix  chain 'A' and resid 199 through 204
    Processing helix  chain 'A' and resid 239 through 250
      removed outlier: 3.800A  pdb=" N   GLN A 250 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 268
    Processing helix  chain 'A' and resid 382 through 391
      removed outlier: 3.599A  pdb=" N   ALA A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 411
      removed outlier: 3.771A  pdb=" N   VAL A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 417
      removed outlier: 3.557A  pdb=" N   GLU A 415 " --> pdb=" O   LYS A 411 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   ILE A 417 " --> pdb=" O   HIS A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 505
      removed outlier: 4.357A  pdb=" N   GLU A 505 " --> pdb=" O   PRO A 502 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 502 through 505'
    Processing helix  chain 'A' and resid 534 through 549
    Processing helix  chain 'A' and resid 670 through 681
      removed outlier: 3.540A  pdb=" N   LEU A 681 " --> pdb=" O   PHE A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 702
      removed outlier: 4.104A  pdb=" N   ILE A 694 " --> pdb=" O   HIS A 690 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   LYS A 695 " --> pdb=" O   VAL A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 719 through 723
    Processing helix  chain 'A' and resid 796 through 800
    Processing helix  chain 'A' and resid 804 through 813
    Processing helix  chain 'A' and resid 832 through 841
    Processing helix  chain 'A' and resid 852 through 867
    Processing helix  chain 'A' and resid 973 through 983
      removed outlier: 3.968A  pdb=" N   ASP A 978 " --> pdb=" O   SER A 974 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   TYR A 983 " --> pdb=" O   THR A 979 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1003
      removed outlier: 3.604A  pdb=" N   GLN A 996 " --> pdb=" O   SER A 992 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1006
      No H-bonds generated for 'chain 'A' and resid 1004 through 1006'
    Processing helix  chain 'A' and resid 1123 through 1134
    Processing helix  chain 'A' and resid 1143 through 1158
    Processing helix  chain 'A' and resid 1268 through 1281
      removed outlier: 3.719A  pdb=" N   HIS A1274 " --> pdb=" O   GLN A1270 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN A1281 " --> pdb=" O   CYS A1277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1292 through 1304
      removed outlier: 3.605A  pdb=" N   TYR A1304 " --> pdb=" O   GLU A1300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1318 through 1322
      removed outlier: 3.689A  pdb=" N   LYS A1321 " --> pdb=" O   TYR A1318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1365 through 1368
    Processing helix  chain 'A' and resid 1369 through 1375
      removed outlier: 3.598A  pdb=" N   HIS A1375 " --> pdb=" O   TYR A1371 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40
    Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 70
      removed outlier: 3.573A  pdb=" N   ARG A  74 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85
    Processing sheet with id=AA4, first strand: chain 'A' and resid 125 through 126
    Processing sheet with id=AA5, first strand: chain 'A' and resid 159 through 162
      removed outlier: 6.479A  pdb=" N   ILE A 208 " --> pdb=" O   ARG A 160 " (cutoff:3.500A)
      removed outlier: 5.079A  pdb=" N   GLY A 162 " --> pdb=" O   TRP A 206 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   TRP A 206 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 173 through 175
    Processing sheet with id=AA7, first strand: chain 'A' and resid 228 through 238
      removed outlier: 3.993A  pdb=" N   ASN A 233 " --> pdb=" O   TYR A 338 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   TYR A 338 " --> pdb=" O   ASN A 233 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   GLN A 235 " --> pdb=" O   LEU A 336 " (cutoff:3.500A)
      removed outlier: 9.402A  pdb=" N   LEU A 336 " --> pdb=" O   GLN A 235 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 275 through 276
    Processing sheet with id=AA9, first strand: chain 'A' and resid 299 through 300
    Processing sheet with id=AB1, first strand: chain 'A' and resid 366 through 368
      removed outlier: 3.853A  pdb=" N   TYR A 483 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLU A 378 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   LEU A 481 " --> pdb=" O   GLU A 378 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL A 484 " --> pdb=" O   TRP A 422 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   GLY A 424 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
      removed outlier: 10.205A  pdb=" N   LYS A 486 " --> pdb=" O   GLY A 424 " (cutoff:3.500A)
      removed outlier: 15.113A  pdb=" N   LYS A 426 " --> pdb=" O   LYS A 486 " (cutoff:3.500A)
      removed outlier: 20.743A  pdb=" N   LYS A 488 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 395 through 396
      removed outlier: 3.979A  pdb=" N   VAL A 484 " --> pdb=" O   TRP A 422 " (cutoff:3.500A)
      removed outlier: 5.642A  pdb=" N   GLY A 424 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
      removed outlier: 10.205A  pdb=" N   LYS A 486 " --> pdb=" O   GLY A 424 " (cutoff:3.500A)
      removed outlier: 15.113A  pdb=" N   LYS A 426 " --> pdb=" O   LYS A 486 " (cutoff:3.500A)
      removed outlier: 20.743A  pdb=" N   LYS A 488 " --> pdb=" O   LYS A 426 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   VAL A 421 " --> pdb=" O   TYR A 465 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A 423 " --> pdb=" O   VAL A 463 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   VAL A 463 " --> pdb=" O   ILE A 423 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   LEU A 425 " --> pdb=" O   ASN A 461 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ASN A 461 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   CYS A 462 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 507 through 508
    Processing sheet with id=AB4, first strand: chain 'A' and resid 570 through 571
      removed outlier: 4.541A  pdb=" N   VAL A 598 " --> pdb=" O   THR A 558 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 655 through 660
      removed outlier: 3.932A  pdb=" N   PHE A 780 " --> pdb=" O   PHE A 660 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 716
      removed outlier: 4.923A  pdb=" N   ALA A 753 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 823 through 831
      removed outlier: 7.722A  pdb=" N   ASP A 828 " --> pdb=" O   LEU A 926 " (cutoff:3.500A)
      removed outlier: 9.579A  pdb=" N   LEU A 926 " --> pdb=" O   ASP A 828 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 849 through 850
    Processing sheet with id=AB9, first strand: chain 'A' and resid 872 through 873
    Processing sheet with id=AC1, first strand: chain 'A' and resid 956 through 958
    Processing sheet with id=AC2, first strand: chain 'A' and resid 970 through 972
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1009 through 1010
    Processing sheet with id=AC4, first strand: chain 'A' and resid 1009 through 1010
    Processing sheet with id=AC5, first strand: chain 'A' and resid 1108 through 1110
    Processing sheet with id=AC6, first strand: chain 'A' and resid 1161 through 1162
    Processing sheet with id=AC7, first strand: chain 'A' and resid 1165 through 1167
    Processing sheet with id=AC8, first strand: chain 'A' and resid 1249 through 1250
    Processing sheet with id=AC9, first strand: chain 'A' and resid 1258 through 1259
      removed outlier: 3.842A  pdb=" N   LEU A1378 " --> pdb=" O   ILE A1259 " (cutoff:3.500A)
      removed outlier: 4.812A  pdb=" N   ALA A1379 " --> pdb=" O   MET A1313 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'A' and resid 1316 through 1317

    274 hydrogen bonds defined for protein.
    705 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: 2.16

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3208
        1.35 -     1.47: 2866
        1.47 -     1.59: 4381
        1.59 -     1.71: 0
        1.71 -     1.83: 79
  Bond restraints: 10534
  Sorted by residual:
  bond pdb=" C1  NAG A1802 "
       pdb=" O5  NAG A1802 "
    ideal  model  delta    sigma   weight residual
    1.406  1.459 -0.053 2.00e-02 2.50e+03 6.92e+00
  bond pdb=" C   THR A 459 "
       pdb=" N   PRO A 460 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 1.11e-02 8.12e+03 3.97e+00
  bond pdb=" C1  BMA B   3 "
       pdb=" C2  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.548 -0.029 2.00e-02 2.50e+03 2.13e+00
  bond pdb=" C1  NAG A1801 "
       pdb=" O5  NAG A1801 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.90e+00
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.88e+00
  ... (remaining 10529 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 14112
        1.69 -     3.38: 223
        3.38 -     5.07: 33
        5.07 -     6.76: 6
        6.76 -     8.45: 2
  Bond angle restraints: 14376
  Sorted by residual:
  angle pdb=" C   TRP A1025 "
        pdb=" N   THR A1026 "
        pdb=" CA  THR A1026 "
      ideal   model   delta    sigma   weight residual
     121.54  127.44   -5.90 1.91e+00 2.74e-01 9.54e+00
  angle pdb=" CA  CYS A 485 "
        pdb=" CB  CYS A 485 "
        pdb=" SG  CYS A 485 "
      ideal   model   delta    sigma   weight residual
     114.40  120.20   -5.80 2.30e+00 1.89e-01 6.35e+00
  angle pdb=" CA  LEU A 654 "
        pdb=" CB  LEU A 654 "
        pdb=" CG  LEU A 654 "
      ideal   model   delta    sigma   weight residual
     116.30  124.75   -8.45 3.50e+00 8.16e-02 5.83e+00
  angle pdb=" N   LEU A1172 "
        pdb=" CA  LEU A1172 "
        pdb=" C   LEU A1172 "
      ideal   model   delta    sigma   weight residual
     113.18  110.00    3.18 1.33e+00 5.65e-01 5.72e+00
  angle pdb=" N   THR A 440 "
        pdb=" CA  THR A 440 "
        pdb=" C   THR A 440 "
      ideal   model   delta    sigma   weight residual
     114.04  111.18    2.86 1.24e+00 6.50e-01 5.31e+00
  ... (remaining 14371 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.55: 5776
       22.55 -    45.10: 364
       45.10 -    67.66: 54
       67.66 -    90.21: 18
       90.21 -   112.76: 7
  Dihedral angle restraints: 6219
    sinusoidal: 2341
      harmonic: 3878
  Sorted by residual:
  dihedral pdb=" CB  CYS A 389 "
           pdb=" SG  CYS A 389 "
           pdb=" SG  CYS A 485 "
           pdb=" CB  CYS A 485 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.27  -87.73     1      1.00e+01 1.00e-02 9.22e+01
  dihedral pdb=" CB  CYS A 317 "
           pdb=" SG  CYS A 317 "
           pdb=" SG  CYS A 332 "
           pdb=" CB  CYS A 332 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.38  -86.38     1      1.00e+01 1.00e-02 8.99e+01
  dihedral pdb=" CB  CYS A 501 "
           pdb=" SG  CYS A 501 "
           pdb=" SG  CYS A 514 "
           pdb=" CB  CYS A 514 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -165.64   79.64     1      1.00e+01 1.00e-02 7.87e+01
  ... (remaining 6216 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1315
       0.054 -    0.108: 205
       0.108 -    0.162: 34
       0.162 -    0.216: 0
       0.216 -    0.269: 1
  Chirality restraints: 1555
  Sorted by residual:
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.54    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  CYS A1211 "
            pdb=" N   CYS A1211 "
            pdb=" C   CYS A1211 "
            pdb=" CB  CYS A1211 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.15 2.00e-01 2.50e+01 5.28e-01
  chirality pdb=" CB  ILE A 737 "
            pdb=" CA  ILE A 737 "
            pdb=" CG1 ILE A 737 "
            pdb=" CG2 ILE A 737 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.28e-01
  ... (remaining 1552 not shown)

  Planarity restraints: 1818
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 967 "   -0.024 5.00e-02 4.00e+02   3.64e-02 2.12e+00
        pdb=" N   PRO A 968 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 968 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 968 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 813 "    0.023 5.00e-02 4.00e+02   3.52e-02 1.98e+00
        pdb=" N   PRO A 814 "   -0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A 814 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 814 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 697 "   -0.013 2.00e-02 2.50e+03   1.06e-02 1.95e+00
        pdb=" CG  PHE A 697 "    0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 697 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 697 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 697 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 697 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 697 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1815 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 2673
        2.79 -     3.32: 8847
        3.32 -     3.85: 16455
        3.85 -     4.37: 18978
        4.37 -     4.90: 32978
  Nonbonded interactions: 79931
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 165 "
            pdb=" OE1 GLN A1301 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   SER A 329 "
            pdb=" OG  SER A 329 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   SER A1097 "
            pdb=" OG  SER A1097 "
     model   vdw
     2.316 3.040
  nonbonded pdb=" OE1 GLU A1195 "
            pdb=" N   ASP A1210 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" NH1 ARG A 160 "
            pdb=" OD2 ASP A 161 "
     model   vdw
     2.324 3.120
  ... (remaining 79926 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.53 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.830
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
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      :  0.002   0.053  10561  Z= 0.122
  Angle     :  0.552   8.452  14434  Z= 0.294
  Chirality :  0.042   0.269   1555
  Planarity :  0.003   0.036   1816
  Dihedral  : 15.001 112.760   3642
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.77 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.97 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole: -4.02 (0.19), residues: 1315
  helix: -1.24 (0.30), residues: 208
  sheet: -2.36 (0.36), residues: 150
  loop : -3.33 (0.16), residues: 957

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 796 
 TYR   0.009   0.001   TYR A 116 
 PHE   0.024   0.001   PHE A 697 
 TRP   0.008   0.001   TRP A1025 
 HIS   0.003   0.000   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10534)
  covalent geometry    : angle       0.54759 (14376)
  SS BOND              : bond        0.00235 (   23)
  SS BOND              : angle       1.22295 (   46)
  hydrogen bonds       : bond        0.14778 (  271)
  hydrogen bonds       : angle       6.22724 (  705)
  link_BETA1-4         : bond        0.00311 (    2)
  link_BETA1-4         : angle       1.12007 (    6)
  link_NAG-ASN         : bond        0.00221 (    2)
  link_NAG-ASN         : angle       0.92706 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 202
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.2372 (OUTLIER) cc_final: 0.1033 (t)
REVERT: A  109 LYS cc_start: 0.6901 (tptt) cc_final: 0.6623 (tptt)
REVERT: A  140 TRP cc_start: 0.6619 (m100) cc_final: 0.6344 (m100)
REVERT: A  222 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6619 (ttpm)
REVERT: A  695 LYS cc_start: 0.5972 (mtpt) cc_final: 0.5410 (mmtm)
REVERT: A  771 ASP cc_start: 0.7619 (m-30) cc_final: 0.7192 (m-30)
REVERT: A  910 LYS cc_start: 0.8137 (ttpm) cc_final: 0.7843 (ttpp)
REVERT: A  911 THR cc_start: 0.8116 (OUTLIER) cc_final: 0.7894 (p)
REVERT: A  996 GLN cc_start: 0.8435 (tp40) cc_final: 0.7982 (tm-30)
REVERT: A 1021 LYS cc_start: 0.7043 (OUTLIER) cc_final: 0.6732 (ptpt)
REVERT: A 1117 ILE cc_start: 0.8628 (mm) cc_final: 0.8421 (mm)
REVERT: A 1136 MET cc_start: 0.7211 (mtt) cc_final: 0.6982 (mtm)
REVERT: A 1266 MET cc_start: 0.3358 (tpt) cc_final: 0.2535 (tpt)
REVERT: A 1313 MET cc_start: 0.7704 (ttt) cc_final: 0.7210 (ttm)
REVERT: A 1361 GLN cc_start: 0.7390 (tm-30) cc_final: 0.7127 (tm-30)
REVERT: A 1370 VAL cc_start: 0.8401 (m) cc_final: 0.8156 (t)
  outliers start: 35
  outliers final: 19
  residues processed: 230
  average time/residue: 0.1191
  time to fit residues: 37.7357
Evaluate side-chains
  144 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 121
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  239 SER
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1021 LYS
Chi-restraints excluded: chain A residue 1069 SER
Chi-restraints excluded: chain A residue 1074 THR
Chi-restraints excluded: chain A residue 1178 ASP
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1317 THR
Chi-restraints excluded: chain A residue 1362 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.0170
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.2022

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
A 113 HIS
A 231 GLN
A 529 ASN
A 538 GLN
A 542 ASN
A 861 ASN
A 993 GLN
A1059 HIS
A1065 ASN
A1173 ASN
A1274 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4560 r_free = 0.4560 target = 0.205844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.174803 restraints weight = 13063.843|
|-----------------------------------------------------------------------------|
r_work (start): 0.4238 rms_B_bonded: 2.66
r_work: 0.4080 rms_B_bonded: 3.23 restraints_weight: 0.5000
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4079
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4079 r_free = 0.4079    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4079 r_free = 0.4079    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4079
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10561  Z= 0.125
  Angle     :  0.595   8.430  14434  Z= 0.299
  Chirality :  0.043   0.200   1555
  Planarity :  0.004   0.046   1816
  Dihedral  :  7.979  58.817   1543
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 21.05 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole: -3.29 (0.20), residues: 1315
  helix: -0.21 (0.33), residues: 211
  sheet: -1.98 (0.38), residues: 150
  loop : -2.93 (0.17), residues: 954

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1290 
 TYR   0.016   0.001   TYR A 116 
 PHE   0.011   0.001   PHE A 998 
 TRP   0.010   0.001   TRP A1124 
 HIS   0.005   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10534)
  covalent geometry    : angle       0.58765 (14376)
  SS BOND              : bond        0.00233 (   23)
  SS BOND              : angle       1.48478 (   46)
  hydrogen bonds       : bond        0.03196 (  271)
  hydrogen bonds       : angle       5.02344 (  705)
  link_BETA1-4         : bond        0.00744 (    2)
  link_BETA1-4         : angle       2.38731 (    6)
  link_NAG-ASN         : bond        0.00221 (    2)
  link_NAG-ASN         : angle       0.99411 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 128
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.2485 (OUTLIER) cc_final: 0.0947 (t)
REVERT: A   67 TRP cc_start: 0.7161 (m100) cc_final: 0.6535 (m100)
REVERT: A   69 TRP cc_start: 0.8685 (m100) cc_final: 0.8409 (m100)
REVERT: A  140 TRP cc_start: 0.6867 (m100) cc_final: 0.6452 (m100)
REVERT: A  406 GLU cc_start: 0.7419 (tm-30) cc_final: 0.7108 (tm-30)
REVERT: A  561 ARG cc_start: 0.6174 (ttp-110) cc_final: 0.5892 (ptm-80)
REVERT: A  590 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6175 (mm-30)
REVERT: A  617 PHE cc_start: 0.5727 (t80) cc_final: 0.5429 (t80)
REVERT: A  695 LYS cc_start: 0.6485 (mtpt) cc_final: 0.5871 (mmtm)
REVERT: A 1136 MET cc_start: 0.7397 (mtt) cc_final: 0.7185 (mtm)
REVERT: A 1266 MET cc_start: 0.3666 (tpt) cc_final: 0.3001 (tpt)
REVERT: A 1313 MET cc_start: 0.8056 (ttt) cc_final: 0.7660 (ttm)
REVERT: A 1370 VAL cc_start: 0.8360 (m) cc_final: 0.7929 (t)
REVERT: A 1374 GLN cc_start: 0.8007 (mt0) cc_final: 0.7788 (mm-40)
  outliers start: 48
  outliers final: 21
  residues processed: 169
  average time/residue: 0.1024
  time to fit residues: 24.9942
Evaluate side-chains
  141 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  590 GLU
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1014 LEU
Chi-restraints excluded: chain A residue 1026 THR
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1241 SER
Chi-restraints excluded: chain A residue 1284 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 107 optimal weight:    5.9990
   chunk 120 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0770
   chunk 114 optimal weight:    0.7980
   chunk 123 optimal weight:    0.8980
   chunk 98 optimal weight:    9.9990
   overall best weight:    1.3542

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

Flipped N/Q/H residues before XYZ refinement:
** A  77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 510 HIS
A 661 HIS
A1065 ASN
A1084 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.204104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.172704 restraints weight = 13028.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.4222 rms_B_bonded: 2.69
r_work: 0.4058 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.4058
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4052
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4052 r_free = 0.4052    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.15   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4052 r_free = 0.4052    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4052
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10561  Z= 0.125
  Angle     :  0.576   8.270  14434  Z= 0.292
  Chirality :  0.042   0.196   1555
  Planarity :  0.004   0.046   1816
  Dihedral  :  6.620  52.883   1525
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 20.85 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole: -2.95 (0.21), residues: 1315
  helix:  0.27 (0.34), residues: 211
  sheet: -1.80 (0.39), residues: 152
  loop : -2.74 (0.18), residues: 952

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A1015 
 TYR   0.015   0.001   TYR A 116 
 PHE   0.029   0.001   PHE A1149 
 TRP   0.009   0.001   TRP A 880 
 HIS   0.003   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10534)
  covalent geometry    : angle       0.56940 (14376)
  SS BOND              : bond        0.00389 (   23)
  SS BOND              : angle       1.48616 (   46)
  hydrogen bonds       : bond        0.03065 (  271)
  hydrogen bonds       : angle       4.83029 (  705)
  link_BETA1-4         : bond        0.00507 (    2)
  link_BETA1-4         : angle       2.01732 (    6)
  link_NAG-ASN         : bond        0.00119 (    2)
  link_NAG-ASN         : angle       1.01881 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 134
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.2695 (OUTLIER) cc_final: 0.0997 (t)
REVERT: A   67 TRP cc_start: 0.7189 (m100) cc_final: 0.6559 (m100)
REVERT: A   69 TRP cc_start: 0.8681 (m100) cc_final: 0.8403 (m100)
REVERT: A  140 TRP cc_start: 0.7035 (m100) cc_final: 0.6350 (m100)
REVERT: A  141 LYS cc_start: 0.7854 (mmmt) cc_final: 0.6322 (mttp)
REVERT: A  406 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7116 (tm-30)
REVERT: A  561 ARG cc_start: 0.6466 (ttp-110) cc_final: 0.6216 (ptm-80)
REVERT: A  617 PHE cc_start: 0.5797 (t80) cc_final: 0.5462 (t80)
REVERT: A 1266 MET cc_start: 0.3750 (tpt) cc_final: 0.3103 (tpt)
REVERT: A 1313 MET cc_start: 0.8107 (ttt) cc_final: 0.7819 (ttm)
REVERT: A 1370 VAL cc_start: 0.8338 (m) cc_final: 0.7990 (t)
REVERT: A 1374 GLN cc_start: 0.8136 (mt0) cc_final: 0.7893 (mm-40)
  outliers start: 49
  outliers final: 32
  residues processed: 178
  average time/residue: 0.1010
  time to fit residues: 25.8311
Evaluate side-chains
  149 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 116
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  226 PHE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  826 VAL
Chi-restraints excluded: chain A residue  832 ASN
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1025 TRP
Chi-restraints excluded: chain A residue 1026 THR
Chi-restraints excluded: chain A residue 1042 SER
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1241 SER
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1326 PHE
Chi-restraints excluded: chain A residue 1380 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 64 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 18 optimal weight:    0.0980
   chunk 110 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    1.2188

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
A1065 ASN
A1173 ASN
A1278 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.203031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.171284 restraints weight = 13054.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.4183 rms_B_bonded: 2.73
r_work: 0.4030 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4074
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4074 r_free = 0.4074    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4074 r_free = 0.4074    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4074
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10561  Z= 0.120
  Angle     :  0.568   8.196  14434  Z= 0.288
  Chirality :  0.042   0.180   1555
  Planarity :  0.004   0.073   1816
  Dihedral  :  6.068  53.365   1521
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 22.05 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole: -2.72 (0.21), residues: 1315
  helix:  0.61 (0.35), residues: 211
  sheet: -1.73 (0.37), residues: 172
  loop : -2.62 (0.18), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1015 
 TYR   0.017   0.001   TYR A1019 
 PHE   0.018   0.001   PHE A 697 
 TRP   0.009   0.001   TRP A 880 
 HIS   0.007   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (10534)
  covalent geometry    : angle       0.56195 (14376)
  SS BOND              : bond        0.00324 (   23)
  SS BOND              : angle       1.41703 (   46)
  hydrogen bonds       : bond        0.02865 (  271)
  hydrogen bonds       : angle       4.73189 (  705)
  link_BETA1-4         : bond        0.00504 (    2)
  link_BETA1-4         : angle       1.81061 (    6)
  link_NAG-ASN         : bond        0.00139 (    2)
  link_NAG-ASN         : angle       1.02320 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 132
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.2702 (OUTLIER) cc_final: 0.2040 (t)
REVERT: A   67 TRP cc_start: 0.7014 (m100) cc_final: 0.6553 (m100)
REVERT: A   69 TRP cc_start: 0.8695 (m100) cc_final: 0.8417 (m100)
REVERT: A  140 TRP cc_start: 0.7076 (m100) cc_final: 0.6374 (m100)
REVERT: A  141 LYS cc_start: 0.7750 (mmmt) cc_final: 0.6493 (mttp)
REVERT: A  406 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7163 (tm-30)
REVERT: A  481 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6912 (pp)
REVERT: A  561 ARG cc_start: 0.6464 (ttp-110) cc_final: 0.6248 (ptm-80)
REVERT: A  617 PHE cc_start: 0.5780 (t80) cc_final: 0.5433 (t80)
REVERT: A 1033 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6918 (p90)
REVERT: A 1136 MET cc_start: 0.7583 (mtt) cc_final: 0.7259 (mtm)
REVERT: A 1266 MET cc_start: 0.3765 (tpt) cc_final: 0.3157 (tpt)
REVERT: A 1313 MET cc_start: 0.8095 (ttt) cc_final: 0.7772 (ttm)
REVERT: A 1370 VAL cc_start: 0.8290 (m) cc_final: 0.7973 (t)
REVERT: A 1374 GLN cc_start: 0.8260 (mt0) cc_final: 0.7960 (mm-40)
  outliers start: 42
  outliers final: 31
  residues processed: 169
  average time/residue: 0.0934
  time to fit residues: 23.3902
Evaluate side-chains
  153 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  226 PHE
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  427 ASN
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  832 ASN
Chi-restraints excluded: chain A residue  852 SER
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1025 TRP
Chi-restraints excluded: chain A residue 1026 THR
Chi-restraints excluded: chain A residue 1033 TYR
Chi-restraints excluded: chain A residue 1042 SER
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1241 SER
Chi-restraints excluded: chain A residue 1326 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    9.9990
   chunk 114 optimal weight:    0.9980
   chunk 95 optimal weight:    4.9990
   chunk 9 optimal weight:   30.0000
   chunk 103 optimal weight:   10.0000
   chunk 110 optimal weight:    0.9990
   chunk 68 optimal weight:    7.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 538 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1065 ASN
A1173 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.202642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.170651 restraints weight = 13054.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.4178 rms_B_bonded: 2.72
r_work: 0.4030 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4046
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4046 r_free = 0.4046    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4046 r_free = 0.4046    target_work(ls_wunit_k1) = 0.156         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4046
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10561  Z= 0.115
  Angle     :  0.558   8.133  14434  Z= 0.284
  Chirality :  0.042   0.172   1555
  Planarity :  0.004   0.067   1816
  Dihedral  :  5.759  53.899   1520
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 21.65 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    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 are not related in a simple way.
  whole: -2.52 (0.22), residues: 1315
  helix:  0.91 (0.35), residues: 210
  sheet: -1.76 (0.36), residues: 180
  loop : -2.47 (0.19), residues: 925

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1015 
 TYR   0.017   0.001   TYR A 548 
 PHE   0.048   0.001   PHE A 958 
 TRP   0.013   0.001   TRP A 912 
 HIS   0.005   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10534)
  covalent geometry    : angle       0.55311 (14376)
  SS BOND              : bond        0.00273 (   23)
  SS BOND              : angle       1.33662 (   46)
  hydrogen bonds       : bond        0.02741 (  271)
  hydrogen bonds       : angle       4.67069 (  705)
  link_BETA1-4         : bond        0.00501 (    2)
  link_BETA1-4         : angle       1.59142 (    6)
  link_NAG-ASN         : bond        0.00175 (    2)
  link_NAG-ASN         : angle       0.99688 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 127
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.2777 (OUTLIER) cc_final: 0.2020 (t)
REVERT: A   67 TRP cc_start: 0.6940 (m100) cc_final: 0.6623 (m100)
REVERT: A  140 TRP cc_start: 0.7070 (m100) cc_final: 0.6473 (m100)
REVERT: A  141 LYS cc_start: 0.7558 (mmmt) cc_final: 0.6348 (mttp)
REVERT: A  406 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7217 (tm-30)
REVERT: A  481 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6896 (pp)
REVERT: A  617 PHE cc_start: 0.5781 (t80) cc_final: 0.5405 (t80)
REVERT: A 1033 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6969 (p90)
REVERT: A 1136 MET cc_start: 0.7664 (mtt) cc_final: 0.7329 (mtm)
REVERT: A 1146 GLN cc_start: 0.7536 (mt0) cc_final: 0.7323 (mt0)
REVERT: A 1266 MET cc_start: 0.3709 (tpt) cc_final: 0.3088 (tpt)
REVERT: A 1313 MET cc_start: 0.8084 (ttt) cc_final: 0.7728 (ttm)
REVERT: A 1370 VAL cc_start: 0.8311 (m) cc_final: 0.8018 (t)
REVERT: A 1374 GLN cc_start: 0.8271 (mt0) cc_final: 0.7968 (mm-40)
  outliers start: 49
  outliers final: 38
  residues processed: 170
  average time/residue: 0.0864
  time to fit residues: 21.9166
Evaluate side-chains
  164 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 123
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  102 SER
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  226 PHE
Chi-restraints excluded: chain A residue  319 ARG
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  427 ASN
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  643 CYS
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  832 ASN
Chi-restraints excluded: chain A residue  852 SER
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1014 LEU
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1033 TYR
Chi-restraints excluded: chain A residue 1042 SER
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1140 SER
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1241 SER
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1326 PHE
Chi-restraints excluded: chain A residue 1380 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 113 optimal weight:    6.9990
   chunk 1 optimal weight:    2.9990
   chunk 61 optimal weight:   10.0000
   chunk 102 optimal weight:    0.7980
   chunk 81 optimal weight:   10.0000
   chunk 51 optimal weight:   10.0000
   chunk 91 optimal weight:    5.9990
   chunk 88 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 93 optimal weight:   10.0000
   chunk 87 optimal weight:    4.9990
   overall best weight:    4.3588

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

Flipped N/Q/H residues before XYZ refinement:
A  33 ASN
A 250 GLN
A 538 GLN
A 542 ASN
A 832 ASN
A1173 ASN
A1257 ASN
A1278 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4398 r_free = 0.4398 target = 0.189815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.157858 restraints weight = 13271.987|
|-----------------------------------------------------------------------------|
r_work (start): 0.4036 rms_B_bonded: 2.69
r_work: 0.3898 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3913
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3913 r_free = 0.3913    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3913 r_free = 0.3913    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3913
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.101  10561  Z= 0.291
  Angle     :  0.760   7.725  14434  Z= 0.388
  Chirality :  0.048   0.272   1555
  Planarity :  0.005   0.062   1816
  Dihedral  :  6.887  57.823   1520
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.65 %
    Favored  : 89.35 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 21.25 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    Twisted Proline : 1.56 %
    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 are not related in a simple way.
  whole: -2.81 (0.21), residues: 1315
  helix:  0.32 (0.34), residues: 211
  sheet: -1.73 (0.36), residues: 178
  loop : -2.63 (0.18), residues: 926

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 669 
 TYR   0.024   0.002   TYR A 888 
 PHE   0.032   0.003   PHE A 958 
 TRP   0.016   0.002   TRP A 277 
 HIS   0.007   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00687 (10534)
  covalent geometry    : angle       0.75006 (14376)
  SS BOND              : bond        0.00467 (   23)
  SS BOND              : angle       2.12106 (   46)
  hydrogen bonds       : bond        0.04223 (  271)
  hydrogen bonds       : angle       5.35555 (  705)
  link_BETA1-4         : bond        0.00116 (    2)
  link_BETA1-4         : angle       2.41298 (    6)
  link_NAG-ASN         : bond        0.00223 (    2)
  link_NAG-ASN         : angle       1.60486 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 118
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.2912 (OUTLIER) cc_final: 0.2480 (t)
REVERT: A   67 TRP cc_start: 0.7148 (m100) cc_final: 0.6864 (m100)
REVERT: A  140 TRP cc_start: 0.7612 (m100) cc_final: 0.6776 (m100)
REVERT: A  141 LYS cc_start: 0.7619 (mmmt) cc_final: 0.6754 (mttp)
REVERT: A  406 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7336 (tm-30)
REVERT: A  466 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6438 (pp)
REVERT: A  481 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7097 (pp)
REVERT: A  838 LEU cc_start: 0.9123 (mm) cc_final: 0.8674 (mm)
REVERT: A  846 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7886 (p90)
REVERT: A 1033 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7415 (p90)
REVERT: A 1117 ILE cc_start: 0.8910 (mm) cc_final: 0.8572 (mt)
REVERT: A 1266 MET cc_start: 0.3996 (tpt) cc_final: 0.3621 (tpt)
REVERT: A 1313 MET cc_start: 0.8090 (ttt) cc_final: 0.7599 (ttm)
REVERT: A 1361 GLN cc_start: 0.7768 (tm-30) cc_final: 0.7273 (tm-30)
REVERT: A 1370 VAL cc_start: 0.8475 (m) cc_final: 0.8203 (t)
REVERT: A 1374 GLN cc_start: 0.8236 (mt0) cc_final: 0.8003 (mm-40)
  outliers start: 64
  outliers final: 45
  residues processed: 173
  average time/residue: 0.0793
  time to fit residues: 20.7467
Evaluate side-chains
  159 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 109
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  226 PHE
Chi-restraints excluded: chain A residue  278 ILE
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  643 CYS
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue  846 PHE
Chi-restraints excluded: chain A residue  852 SER
Chi-restraints excluded: chain A residue  878 SER
Chi-restraints excluded: chain A residue  880 TRP
Chi-restraints excluded: chain A residue  907 MET
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  956 ILE
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1033 TYR
Chi-restraints excluded: chain A residue 1042 SER
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1140 SER
Chi-restraints excluded: chain A residue 1178 ASP
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1241 SER
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1326 PHE
Chi-restraints excluded: chain A residue 1380 CYS
Chi-restraints excluded: chain A residue 1382 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 69 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 960 ASN
A1065 ASN
A1278 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.193826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.160486 restraints weight = 13069.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 2.90
r_work: 0.3941 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3956
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3956 r_free = 0.3956    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3956 r_free = 0.3956    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3956
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10561  Z= 0.162
  Angle     :  0.628   7.799  14434  Z= 0.320
  Chirality :  0.044   0.208   1555
  Planarity :  0.004   0.054   1816
  Dihedral  :  6.408  57.941   1519
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.76 %
    Favored  : 92.24 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 21.75 %
    Favored  : 72.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    Twisted Proline : 1.56 %
    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 are not related in a simple way.
  whole: -2.57 (0.21), residues: 1315
  helix:  0.61 (0.35), residues: 213
  sheet: -1.60 (0.37), residues: 177
  loop : -2.49 (0.18), residues: 925

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1015 
 TYR   0.016   0.001   TYR A 548 
 PHE   0.030   0.002   PHE A 958 
 TRP   0.023   0.001   TRP A 912 
 HIS   0.004   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10534)
  covalent geometry    : angle       0.62061 (14376)
  SS BOND              : bond        0.00513 (   23)
  SS BOND              : angle       1.63570 (   46)
  hydrogen bonds       : bond        0.03202 (  271)
  hydrogen bonds       : angle       5.06540 (  705)
  link_BETA1-4         : bond        0.00629 (    2)
  link_BETA1-4         : angle       1.82023 (    6)
  link_NAG-ASN         : bond        0.00155 (    2)
  link_NAG-ASN         : angle       1.31497 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 123
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.3100 (OUTLIER) cc_final: 0.2635 (t)
REVERT: A   67 TRP cc_start: 0.7153 (m100) cc_final: 0.6791 (m100)
REVERT: A  140 TRP cc_start: 0.7571 (m100) cc_final: 0.6727 (m100)
REVERT: A  141 LYS cc_start: 0.7516 (mmmt) cc_final: 0.6822 (mttp)
REVERT: A  406 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7211 (tm-30)
REVERT: A  466 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6417 (pp)
REVERT: A  481 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7008 (pp)
REVERT: A  838 LEU cc_start: 0.9073 (mm) cc_final: 0.8635 (mm)
REVERT: A 1033 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.7288 (p90)
REVERT: A 1117 ILE cc_start: 0.8896 (mm) cc_final: 0.8564 (mt)
REVERT: A 1266 MET cc_start: 0.3593 (tpt) cc_final: 0.2879 (tpt)
REVERT: A 1313 MET cc_start: 0.8021 (ttt) cc_final: 0.7575 (ttm)
REVERT: A 1370 VAL cc_start: 0.8360 (m) cc_final: 0.8106 (t)
REVERT: A 1374 GLN cc_start: 0.8233 (mt0) cc_final: 0.8031 (mm110)
  outliers start: 61
  outliers final: 47
  residues processed: 175
  average time/residue: 0.0799
  time to fit residues: 21.5930
Evaluate side-chains
  164 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 113
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  226 PHE
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  643 CYS
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue  852 SER
Chi-restraints excluded: chain A residue  878 SER
Chi-restraints excluded: chain A residue  882 ILE
Chi-restraints excluded: chain A residue  904 CYS
Chi-restraints excluded: chain A residue  907 MET
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue  995 GLU
Chi-restraints excluded: chain A residue 1014 LEU
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1033 TYR
Chi-restraints excluded: chain A residue 1042 SER
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1140 SER
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1241 SER
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1326 PHE
Chi-restraints excluded: chain A residue 1380 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 79 optimal weight:   10.0000
   chunk 22 optimal weight:    4.9990
   chunk 74 optimal weight:    8.9990
   chunk 122 optimal weight:    5.9990
   chunk 47 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 37 optimal weight:    8.9990
   chunk 83 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    4.5388

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

Flipped N/Q/H residues before XYZ refinement:
A  72 GLN
A 369 ASN
A 960 ASN
A1065 ASN
A1153 GLN
A1278 GLN
A1306 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.188233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.158268 restraints weight = 13229.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 2.40
r_work: 0.3879 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3914
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3914 r_free = 0.3914    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3914
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.102  10561  Z= 0.290
  Angle     :  0.754   8.327  14434  Z= 0.385
  Chirality :  0.048   0.263   1555
  Planarity :  0.005   0.076   1816
  Dihedral  :  6.915  59.186   1519
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.10 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  6.95 %
    Allowed  : 21.45 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    Twisted Proline : 1.56 %
    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 are not related in a simple way.
  whole: -2.71 (0.21), residues: 1315
  helix:  0.33 (0.35), residues: 212
  sheet: -1.72 (0.36), residues: 183
  loop : -2.53 (0.18), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 669 
 TYR   0.023   0.002   TYR A 888 
 PHE   0.029   0.003   PHE A 697 
 TRP   0.016   0.002   TRP A 912 
 HIS   0.006   0.001   HIS A 294 

Details of bonding type rmsd
  covalent geometry    : bond        0.00692 (10534)
  covalent geometry    : angle       0.74278 (14376)
  SS BOND              : bond        0.00437 (   23)
  SS BOND              : angle       2.17505 (   46)
  hydrogen bonds       : bond        0.03871 (  271)
  hydrogen bonds       : angle       5.40109 (  705)
  link_BETA1-4         : bond        0.00661 (    2)
  link_BETA1-4         : angle       2.25890 (    6)
  link_NAG-ASN         : bond        0.00070 (    2)
  link_NAG-ASN         : angle       1.66903 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 113
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.2904 (OUTLIER) cc_final: 0.2442 (t)
REVERT: A  140 TRP cc_start: 0.7756 (m100) cc_final: 0.6965 (m100)
REVERT: A  141 LYS cc_start: 0.7588 (mmmt) cc_final: 0.6931 (mttp)
REVERT: A  406 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7313 (tm-30)
REVERT: A  466 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6614 (pp)
REVERT: A  481 LEU cc_start: 0.7500 (OUTLIER) cc_final: 0.7140 (pp)
REVERT: A  771 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7724 (m-30)
REVERT: A  778 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.7479 (mtm-85)
REVERT: A  838 LEU cc_start: 0.9136 (mm) cc_final: 0.8690 (mm)
REVERT: A 1033 TYR cc_start: 0.7825 (OUTLIER) cc_final: 0.7380 (p90)
REVERT: A 1117 ILE cc_start: 0.8899 (mm) cc_final: 0.8580 (mt)
REVERT: A 1266 MET cc_start: 0.3553 (tpt) cc_final: 0.3347 (tpt)
REVERT: A 1313 MET cc_start: 0.8095 (ttt) cc_final: 0.7602 (ttm)
REVERT: A 1370 VAL cc_start: 0.8451 (m) cc_final: 0.8201 (t)
REVERT: A 1374 GLN cc_start: 0.8252 (mt0) cc_final: 0.8028 (mm-40)
  outliers start: 70
  outliers final: 48
  residues processed: 170
  average time/residue: 0.0899
  time to fit residues: 22.8605
Evaluate side-chains
  166 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 112
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  134 SER
Chi-restraints excluded: chain A residue  226 PHE
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  466 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  643 CYS
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  778 ARG
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue  852 SER
Chi-restraints excluded: chain A residue  878 SER
Chi-restraints excluded: chain A residue  880 TRP
Chi-restraints excluded: chain A residue  907 MET
Chi-restraints excluded: chain A residue  911 THR
Chi-restraints excluded: chain A residue  929 ILE
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1033 TYR
Chi-restraints excluded: chain A residue 1042 SER
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1140 SER
Chi-restraints excluded: chain A residue 1178 ASP
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1241 SER
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1326 PHE
Chi-restraints excluded: chain A residue 1380 CYS
Chi-restraints excluded: chain A residue 1382 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 95 optimal weight:    6.9990
   chunk 88 optimal weight:    6.9990
   chunk 107 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0870
   chunk 61 optimal weight:    2.9990
   chunk 102 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 114 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   overall best weight:    0.9160

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

Flipped N/Q/H residues before XYZ refinement:
A 960 ASN
A1065 ASN
A1153 GLN
A1278 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.196384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.163243 restraints weight = 13004.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 2.54
r_work: 0.3979 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3992
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3992 r_free = 0.3992    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3992 r_free = 0.3992    target_work(ls_wunit_k1) = 0.151         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3992
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10561  Z= 0.122
  Angle     :  0.612   7.826  14434  Z= 0.314
  Chirality :  0.043   0.182   1555
  Planarity :  0.004   0.063   1816
  Dihedral  :  6.374  59.525   1519
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 23.34 %
    Favored  : 71.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    Twisted Proline : 1.56 %
    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 are not related in a simple way.
  whole: -2.41 (0.22), residues: 1315
  helix:  0.72 (0.35), residues: 214
  sheet: -1.58 (0.36), residues: 185
  loop : -2.35 (0.19), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1015 
 TYR   0.019   0.001   TYR A 548 
 PHE   0.030   0.002   PHE A 958 
 TRP   0.056   0.001   TRP A  67 
 HIS   0.007   0.001   HIS A  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10534)
  covalent geometry    : angle       0.60636 (14376)
  SS BOND              : bond        0.00405 (   23)
  SS BOND              : angle       1.44518 (   46)
  hydrogen bonds       : bond        0.02943 (  271)
  hydrogen bonds       : angle       4.98946 (  705)
  link_BETA1-4         : bond        0.00579 (    2)
  link_BETA1-4         : angle       1.63856 (    6)
  link_NAG-ASN         : bond        0.00317 (    2)
  link_NAG-ASN         : angle       1.23520 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 119
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.3100 (OUTLIER) cc_final: 0.2763 (t)
REVERT: A  140 TRP cc_start: 0.7564 (m100) cc_final: 0.6805 (m100)
REVERT: A  141 LYS cc_start: 0.7356 (mmmt) cc_final: 0.6804 (mttp)
REVERT: A  406 GLU cc_start: 0.7453 (tm-30) cc_final: 0.7159 (tm-30)
REVERT: A  481 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.7017 (pp)
REVERT: A  695 LYS cc_start: 0.6827 (mmmt) cc_final: 0.5828 (mmmt)
REVERT: A  771 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7595 (m-30)
REVERT: A  838 LEU cc_start: 0.9090 (mm) cc_final: 0.8724 (mm)
REVERT: A 1033 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.7398 (p90)
REVERT: A 1117 ILE cc_start: 0.8840 (mm) cc_final: 0.8505 (mt)
REVERT: A 1266 MET cc_start: 0.3325 (tpt) cc_final: 0.2709 (tpt)
REVERT: A 1313 MET cc_start: 0.8011 (ttt) cc_final: 0.7677 (ttm)
REVERT: A 1370 VAL cc_start: 0.8329 (m) cc_final: 0.8099 (t)
REVERT: A 1374 GLN cc_start: 0.8221 (mt0) cc_final: 0.7990 (mm110)
  outliers start: 50
  outliers final: 36
  residues processed: 162
  average time/residue: 0.0825
  time to fit residues: 20.4136
Evaluate side-chains
  156 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 116
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  643 CYS
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue  852 SER
Chi-restraints excluded: chain A residue  878 SER
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1033 TYR
Chi-restraints excluded: chain A residue 1042 SER
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1140 SER
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1241 SER
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1326 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 59 optimal weight:   30.0000
   chunk 94 optimal weight:    1.9990
   chunk 99 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0670
   chunk 117 optimal weight:    5.9990
   chunk 102 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 10 optimal weight:    9.9990
   chunk 114 optimal weight:    0.9990
   overall best weight:    2.2126

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

Flipped N/Q/H residues before XYZ refinement:
A 960 ASN
A1065 ASN
A1278 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.193240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.160058 restraints weight = 12885.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.51
r_work: 0.3942 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3957 r_free = 0.3957    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3957 r_free = 0.3957    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7517
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10561  Z= 0.167
  Angle     :  0.638   8.159  14434  Z= 0.326
  Chirality :  0.044   0.207   1555
  Planarity :  0.004   0.060   1816
  Dihedral  :  6.381  58.371   1519
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.90 %
    Favored  : 91.10 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 23.54 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    Twisted Proline : 1.56 %
    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 are not related in a simple way.
  whole: -2.39 (0.22), residues: 1315
  helix:  0.73 (0.35), residues: 213
  sheet: -1.56 (0.36), residues: 188
  loop : -2.34 (0.19), residues: 914

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A1015 
 TYR   0.016   0.001   TYR A 548 
 PHE   0.028   0.002   PHE A 958 
 TRP   0.038   0.001   TRP A 912 
 HIS   0.004   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (10534)
  covalent geometry    : angle       0.63108 (14376)
  SS BOND              : bond        0.00309 (   23)
  SS BOND              : angle       1.65734 (   46)
  hydrogen bonds       : bond        0.03151 (  271)
  hydrogen bonds       : angle       5.02373 (  705)
  link_BETA1-4         : bond        0.00559 (    2)
  link_BETA1-4         : angle       1.80536 (    6)
  link_NAG-ASN         : bond        0.00068 (    2)
  link_NAG-ASN         : angle       1.41376 (    6)

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

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

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2630 Ramachandran restraints generated.
    1315 Oldfield, 0 Emsley, 1315 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 116
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 CYS cc_start: 0.3089 (OUTLIER) cc_final: 0.2738 (t)
REVERT: A  140 TRP cc_start: 0.7737 (m100) cc_final: 0.6901 (m100)
REVERT: A  141 LYS cc_start: 0.7461 (mmmt) cc_final: 0.6886 (mttp)
REVERT: A  406 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7223 (tm-30)
REVERT: A  481 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.7002 (pp)
REVERT: A  695 LYS cc_start: 0.6879 (mmmt) cc_final: 0.5867 (mmmt)
REVERT: A  771 ASP cc_start: 0.8166 (OUTLIER) cc_final: 0.7639 (m-30)
REVERT: A  838 LEU cc_start: 0.9120 (mm) cc_final: 0.8721 (mm)
REVERT: A 1117 ILE cc_start: 0.8867 (mm) cc_final: 0.8526 (mt)
REVERT: A 1266 MET cc_start: 0.3437 (tpt) cc_final: 0.2779 (tpt)
REVERT: A 1313 MET cc_start: 0.8043 (ttt) cc_final: 0.7697 (ttm)
REVERT: A 1370 VAL cc_start: 0.8372 (m) cc_final: 0.8127 (t)
REVERT: A 1374 GLN cc_start: 0.8210 (mt0) cc_final: 0.7971 (mm110)
  outliers start: 49
  outliers final: 41
  residues processed: 159
  average time/residue: 0.0815
  time to fit residues: 19.7137
Evaluate side-chains
  157 residues out of total 1190 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 113
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ASP
Chi-restraints excluded: chain A residue   55 VAL
Chi-restraints excluded: chain A residue   59 CYS
Chi-restraints excluded: chain A residue  105 MET
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  361 CYS
Chi-restraints excluded: chain A residue  389 CYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  412 LEU
Chi-restraints excluded: chain A residue  423 ILE
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  593 SER
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  643 CYS
Chi-restraints excluded: chain A residue  666 VAL
Chi-restraints excluded: chain A residue  691 VAL
Chi-restraints excluded: chain A residue  694 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  725 SER
Chi-restraints excluded: chain A residue  734 VAL
Chi-restraints excluded: chain A residue  736 THR
Chi-restraints excluded: chain A residue  771 ASP
Chi-restraints excluded: chain A residue  775 ILE
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  821 SER
Chi-restraints excluded: chain A residue  852 SER
Chi-restraints excluded: chain A residue  878 SER
Chi-restraints excluded: chain A residue  960 ASN
Chi-restraints excluded: chain A residue  966 ILE
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue  994 ILE
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1042 SER
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1140 SER
Chi-restraints excluded: chain A residue 1221 TYR
Chi-restraints excluded: chain A residue 1241 SER
Chi-restraints excluded: chain A residue 1284 SER
Chi-restraints excluded: chain A residue 1326 PHE
Chi-restraints excluded: chain A residue 1382 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 53 optimal weight:   30.0000
   chunk 111 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 116 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 124 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 123 optimal weight:    0.0060
   overall best weight:    0.7602

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

Flipped N/Q/H residues before XYZ refinement:
A 960 ASN
A1065 ASN
A1278 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.197625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.163266 restraints weight = 13050.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.4113 rms_B_bonded: 2.63
r_work: 0.3988 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4001 r_free = 0.4001    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4001 r_free = 0.4001    target_work(ls_wunit_k1) = 0.152         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10561  Z= 0.112
  Angle     :  0.602   8.311  14434  Z= 0.307
  Chirality :  0.042   0.166   1555
  Planarity :  0.004   0.057   1816
  Dihedral  :  6.120  55.083   1519
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.92 %
    Favored  : 93.08 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 24.63 %
    Favored  : 71.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.16 %
    Twisted Proline : 1.56 %
    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 are not related in a simple way.
  whole: -2.24 (0.22), residues: 1315
  helix:  0.93 (0.35), residues: 213
  sheet: -1.53 (0.36), residues: 190
  loop : -2.24 (0.19), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 778 
 TYR   0.019   0.001   TYR A 548 
 PHE   0.032   0.001   PHE A 958 
 TRP   0.033   0.001   TRP A 912 
 HIS   0.005   0.001   HIS A  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10534)
  covalent geometry    : angle       0.59720 (14376)
  SS BOND              : bond        0.00256 (   23)
  SS BOND              : angle       1.28897 (   46)
  hydrogen bonds       : bond        0.02767 (  271)
  hydrogen bonds       : angle       4.88870 (  705)
  link_BETA1-4         : bond        0.00475 (    2)
  link_BETA1-4         : angle       1.51613 (    6)
  link_NAG-ASN         : bond        0.00272 (    2)
  link_NAG-ASN         : angle       1.21044 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2453.54 seconds
wall clock time: 42 minutes 51.22 seconds (2571.22 seconds total)