Starting phenix.real_space_refine
on Wed Jul 30 04:49:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wl6_37612/07_2025/8wl6_37612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wl6_37612/07_2025/8wl6_37612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wl6_37612/07_2025/8wl6_37612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wl6_37612/07_2025/8wl6_37612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wl6_37612/07_2025/8wl6_37612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wl6_37612/07_2025/8wl6_37612.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.048
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      73      5.16       5
     C    7783      2.51       5
     N    1998      2.21       5
     O    2068      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11922
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 11922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1489, 11922
          Classifications: {'peptide': 1489}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 66, 'TRANS': 1422}
          Chain breaks: 8
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 241
          Unresolved non-hydrogen angles: 304
          Unresolved non-hydrogen dihedrals: 206
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 3, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 161
  Time building chain proxies: 6.71, per 1000 atoms: 0.56
  Number of scatterers: 11922
  At special positions: 0
  Unit cell: (112.2, 118.8, 132, 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      73     16.00
     O    2068      8.00
     N    1998      7.00
     C    7783      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1328 " - pdb=" SG  CYS A1345 " 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
  Time building additional restraints: 2.68
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2828

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 2 sheets defined
      64.8% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 148 through 153
      removed outlier: 3.518A  pdb=" N   THR A 152 " --> pdb=" O   TYR A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 176
      removed outlier: 3.561A  pdb=" N   ILE A 164 " --> pdb=" O   SER A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 197
      removed outlier: 3.635A  pdb=" N   MET A 182 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ARG A 183 " --> pdb=" O   ARG A 179 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ASN A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 214
      removed outlier: 3.883A  pdb=" N   LEU A 206 " --> pdb=" O   PRO A 202 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   LEU A 207 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 229
      removed outlier: 3.972A  pdb=" N   LYS A 223 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 242
      removed outlier: 3.556A  pdb=" N   ILE A 236 " --> pdb=" O   MET A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 248
      removed outlier: 3.646A  pdb=" N   LEU A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.626A  pdb=" N   LYS A 275 " --> pdb=" O   THR A 272 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLU A 277 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 295
      removed outlier: 3.946A  pdb=" N   ALA A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 313
    Processing helix  chain 'A' and resid 317 through 320
      removed outlier: 3.573A  pdb=" N   PHE A 320 " --> pdb=" O   GLN A 317 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 317 through 320'
    Processing helix  chain 'A' and resid 321 through 338
      removed outlier: 3.657A  pdb=" N   LEU A 325 " --> pdb=" O   THR A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 369
      removed outlier: 3.509A  pdb=" N   ASN A 355 " --> pdb=" O   GLY A 351 " (cutoff:3.500A)
      Proline residue:  A 360  - end of helix
      removed outlier: 3.812A  pdb=" N   VAL A 369 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 399
      removed outlier: 4.150A  pdb=" N   TYR A 399 " --> pdb=" O   GLN A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 404
      removed outlier: 3.737A  pdb=" N   ILE A 403 " --> pdb=" O   TYR A 399 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   ALA A 404 " --> pdb=" O   PRO A 400 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 399 through 404'
    Processing helix  chain 'A' and resid 413 through 417
    Processing helix  chain 'A' and resid 444 through 452
      removed outlier: 3.502A  pdb=" N   LEU A 448 " --> pdb=" O   THR A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 470
    Processing helix  chain 'A' and resid 489 through 518
      removed outlier: 3.673A  pdb=" N   VAL A 518 " --> pdb=" O   GLU A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 551
      Proline residue:  A 545  - end of helix
    Processing helix  chain 'A' and resid 561 through 583
    Processing helix  chain 'A' and resid 615 through 654
      removed outlier: 4.347A  pdb=" N   TRP A 619 " --> pdb=" O   GLY A 615 " (cutoff:3.500A)
      Proline residue:  A 647  - end of helix
      removed outlier: 3.743A  pdb=" N   THR A 654 " --> pdb=" O   ILE A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 666 through 711
      removed outlier: 3.716A  pdb=" N   LYS A 670 " --> pdb=" O   ALA A 666 " (cutoff:3.500A)
      Proline residue:  A 673  - end of helix
      removed outlier: 4.058A  pdb=" N   LEU A 677 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   GLY A 678 " --> pdb=" O   LYS A 674 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   LEU A 679 " --> pdb=" O   ILE A 675 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   VAL A 680 " --> pdb=" O   VAL A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 725
      removed outlier: 4.068A  pdb=" N   ILE A 722 " --> pdb=" O   PRO A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 734
      removed outlier: 3.624A  pdb=" N   ARG A 729 " --> pdb=" O   ARG A 725 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 764
      removed outlier: 3.973A  pdb=" N   GLU A 764 " --> pdb=" O   SER A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 776
      removed outlier: 4.180A  pdb=" N   GLN A 773 " --> pdb=" O   ILE A 769 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LYS A 774 " --> pdb=" O   ASP A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 801 through 805
      removed outlier: 3.943A  pdb=" N   PHE A 804 " --> pdb=" O   ASP A 801 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   GLU A 805 " --> pdb=" O   ASN A 802 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 801 through 805'
    Processing helix  chain 'A' and resid 820 through 826
    Processing helix  chain 'A' and resid 835 through 839
    Processing helix  chain 'A' and resid 856 through 862
      removed outlier: 3.645A  pdb=" N   ILE A 860 " --> pdb=" O   SER A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 871 through 879
    Processing helix  chain 'A' and resid 882 through 892
    Processing helix  chain 'A' and resid 932 through 945
    Processing helix  chain 'A' and resid 949 through 958
      removed outlier: 3.765A  pdb=" N   THR A 953 " --> pdb=" O   THR A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 972
      removed outlier: 4.352A  pdb=" N   ARG A 962 " --> pdb=" O   MET A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 980
      removed outlier: 4.215A  pdb=" N   GLN A 977 " --> pdb=" O   PRO A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 997
      removed outlier: 3.635A  pdb=" N   LEU A 990 " --> pdb=" O   LEU A 986 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LYS A 997 " --> pdb=" O   MET A 993 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1025
    Processing helix  chain 'A' and resid 1081 through 1090
      removed outlier: 3.585A  pdb=" N   ALA A1089 " --> pdb=" O   ASN A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1093
      No H-bonds generated for 'chain 'A' and resid 1091 through 1093'
    Processing helix  chain 'A' and resid 1108 through 1113
      removed outlier: 3.961A  pdb=" N   LEU A1113 " --> pdb=" O   GLU A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1114 through 1120
    Processing helix  chain 'A' and resid 1121 through 1123
      No H-bonds generated for 'chain 'A' and resid 1121 through 1123'
    Processing helix  chain 'A' and resid 1201 through 1206
      removed outlier: 3.798A  pdb=" N   THR A1206 " --> pdb=" O   THR A1202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1233
      removed outlier: 3.697A  pdb=" N   GLY A1226 " --> pdb=" O   ASP A1222 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A1233 " --> pdb=" O   ALA A1229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1268
    Processing helix  chain 'A' and resid 1272 through 1280
      removed outlier: 3.869A  pdb=" N   TYR A1276 " --> pdb=" O   SER A1272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1292
    Processing helix  chain 'A' and resid 1293 through 1325
      removed outlier: 4.145A  pdb=" N   PHE A1297 " --> pdb=" O   ALA A1293 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   HIS A1298 " --> pdb=" O   HIS A1294 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A1304 " --> pdb=" O   ASN A1300 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   GLN A1305 " --> pdb=" O   ASN A1301 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A1306 " --> pdb=" O   LEU A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1348 through 1378
      removed outlier: 4.001A  pdb=" N   VAL A1352 " --> pdb=" O   PHE A1348 " (cutoff:3.500A)
      Proline residue:  A1372  - end of helix
    Processing helix  chain 'A' and resid 1379 through 1390
    Processing helix  chain 'A' and resid 1437 through 1467
      removed outlier: 3.804A  pdb=" N   LEU A1441 " --> pdb=" O   PRO A1437 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   MET A1452 " --> pdb=" O   SER A1448 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   ARG A1455 " --> pdb=" O   TYR A1451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1471 through 1490
      removed outlier: 3.632A  pdb=" N   ALA A1477 " --> pdb=" O   LEU A1473 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   SER A1478 " --> pdb=" O   TRP A1474 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   LEU A1479 " --> pdb=" O   PHE A1475 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   SER A1480 " --> pdb=" O   TRP A1476 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   SER A1481 " --> pdb=" O   ALA A1477 " (cutoff:3.500A)
      Proline residue:  A1486  - end of helix
    Processing helix  chain 'A' and resid 1495 through 1518
    Processing helix  chain 'A' and resid 1556 through 1583
      removed outlier: 3.793A  pdb=" N   LEU A1560 " --> pdb=" O   HIS A1556 " (cutoff:3.500A)
      Proline residue:  A1567  - end of helix
      removed outlier: 3.690A  pdb=" N   ASN A1583 " --> pdb=" O   PHE A1579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1597 through 1627
      removed outlier: 3.890A  pdb=" N   ARG A1601 " --> pdb=" O   ASN A1597 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   ILE A1603 " --> pdb=" O   VAL A1599 " (cutoff:3.500A)
      Proline residue:  A1609  - end of helix
      removed outlier: 3.787A  pdb=" N   VAL A1616 " --> pdb=" O   VAL A1612 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A1617 " --> pdb=" O   ASN A1613 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1638 through 1665
      removed outlier: 3.777A  pdb=" N   GLU A1665 " --> pdb=" O   MET A1661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1668 through 1696
      removed outlier: 3.746A  pdb=" N   MET A1672 " --> pdb=" O   ASN A1668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1723 through 1759
      Proline residue:  A1756  - end of helix
      removed outlier: 4.180A  pdb=" N   ILE A1759 " --> pdb=" O   LEU A1755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1765 through 1779
      Proline residue:  A1776  - end of helix
    Processing helix  chain 'A' and resid 1790 through 1825
      Proline residue:  A1818  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 370 through 373
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1068 through 1069
      removed outlier: 4.217A  pdb=" N   PHE A1068 " --> pdb=" O   LEU A1051 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU A1051 " --> pdb=" O   PHE A1068 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ARG A1046 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU A1036 " --> pdb=" O   ARG A1046 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASP A1034 " --> pdb=" O   TYR A1048 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLN A1029 " --> pdb=" O   PHE A1000 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   LEU A1033 " --> pdb=" O   MET A1004 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   PHE A 842 " --> pdb=" O   LYS A 999 " (cutoff:3.500A)
      removed outlier: 7.928A  pdb=" N   LEU A1001 " --> pdb=" O   PHE A 842 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL A 844 " --> pdb=" O   LEU A1001 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   SER A1003 " --> pdb=" O   VAL A 844 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   THR A 846 " --> pdb=" O   SER A1003 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   ALA A1149 " --> pdb=" O   ASN A1200 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   VAL A1148 " --> pdb=" O   ARG A1235 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   LYS A1237 " --> pdb=" O   VAL A1148 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   ILE A1150 " --> pdb=" O   LYS A1237 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   CYS A1239 " --> pdb=" O   ILE A1150 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   GLY A1152 " --> pdb=" O   CYS A1239 " (cutoff:3.500A)

    641 hydrogen bonds defined for protein.
    1896 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: 3.68

  Time building geometry restraints manager: 3.24 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3742
        1.34 -     1.46: 2984
        1.46 -     1.58: 5396
        1.58 -     1.70: 0
        1.70 -     1.82: 116
  Bond restraints: 12238
  Sorted by residual:
  bond pdb=" C   LEU A 642 "
       pdb=" O   LEU A 642 "
    ideal  model  delta    sigma   weight residual
    1.237  1.259 -0.023 1.16e-02 7.43e+03 3.87e+00
  bond pdb=" CA  VAL A1371 "
       pdb=" C   VAL A1371 "
    ideal  model  delta    sigma   weight residual
    1.520  1.533 -0.013 8.80e-03 1.29e+04 2.24e+00
  bond pdb=" C   PHE A 685 "
       pdb=" O   PHE A 685 "
    ideal  model  delta    sigma   weight residual
    1.236  1.253 -0.017 1.15e-02 7.56e+03 2.15e+00
  bond pdb=" CA  VAL A1371 "
       pdb=" CB  VAL A1371 "
    ideal  model  delta    sigma   weight residual
    1.534  1.544 -0.009 6.80e-03 2.16e+04 1.84e+00
  bond pdb=" CA  ASP A 646 "
       pdb=" C   ASP A 646 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.017 1.26e-02 6.30e+03 1.74e+00
  ... (remaining 12233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 16414
        2.27 -     4.55: 173
        4.55 -     6.82: 25
        6.82 -     9.09: 5
        9.09 -    11.36: 1
  Bond angle restraints: 16618
  Sorted by residual:
  angle pdb=" N   PRO A1782 "
        pdb=" CA  PRO A1782 "
        pdb=" CB  PRO A1782 "
      ideal   model   delta    sigma   weight residual
     103.08  111.50   -8.42 9.70e-01 1.06e+00 7.54e+01
  angle pdb=" N   PRO A1783 "
        pdb=" CA  PRO A1783 "
        pdb=" CB  PRO A1783 "
      ideal   model   delta    sigma   weight residual
     103.25  110.54   -7.29 1.05e+00 9.07e-01 4.82e+01
  angle pdb=" N   PRO A 810 "
        pdb=" CA  PRO A 810 "
        pdb=" CB  PRO A 810 "
      ideal   model   delta    sigma   weight residual
     103.25  109.91   -6.66 1.05e+00 9.07e-01 4.02e+01
  angle pdb=" N   PRO A1776 "
        pdb=" CA  PRO A1776 "
        pdb=" CB  PRO A1776 "
      ideal   model   delta    sigma   weight residual
     103.39  110.20   -6.81 1.08e+00 8.57e-01 3.97e+01
  angle pdb=" CA  PRO A 647 "
        pdb=" N   PRO A 647 "
        pdb=" CD  PRO A 647 "
      ideal   model   delta    sigma   weight residual
     112.00  105.58    6.42 1.40e+00 5.10e-01 2.10e+01
  ... (remaining 16613 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 6185
       17.98 -    35.96: 772
       35.96 -    53.93: 204
       53.93 -    71.91: 28
       71.91 -    89.89: 8
  Dihedral angle restraints: 7197
    sinusoidal: 2821
      harmonic: 4376
  Sorted by residual:
  dihedral pdb=" CA  TYR A 662 "
           pdb=" C   TYR A 662 "
           pdb=" N   TRP A 663 "
           pdb=" CA  TRP A 663 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.52   22.48     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  ALA A 551 "
           pdb=" C   ALA A 551 "
           pdb=" N   TYR A 552 "
           pdb=" CA  TYR A 552 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.99   21.01     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  TYR A 552 "
           pdb=" C   TYR A 552 "
           pdb=" N   ASP A 553 "
           pdb=" CA  ASP A 553 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.72   20.28     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 7194 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1414
       0.046 -    0.091: 355
       0.091 -    0.137: 70
       0.137 -    0.183: 2
       0.183 -    0.229: 4
  Chirality restraints: 1845
  Sorted by residual:
  chirality pdb=" CA  PRO A1776 "
            pdb=" N   PRO A1776 "
            pdb=" C   PRO A1776 "
            pdb=" CB  PRO A1776 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CA  PRO A 810 "
            pdb=" N   PRO A 810 "
            pdb=" C   PRO A 810 "
            pdb=" CB  PRO A 810 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  PRO A1783 "
            pdb=" N   PRO A1783 "
            pdb=" C   PRO A1783 "
            pdb=" CB  PRO A1783 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1842 not shown)

  Planarity restraints: 2087
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 646 "    0.074 5.00e-02 4.00e+02   1.09e-01 1.89e+01
        pdb=" N   PRO A 647 "   -0.188 5.00e-02 4.00e+02
        pdb=" CA  PRO A 647 "    0.055 5.00e-02 4.00e+02
        pdb=" CD  PRO A 647 "    0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A1447 "   -0.013 2.00e-02 2.50e+03   2.54e-02 6.45e+00
        pdb=" C   GLY A1447 "    0.044 2.00e-02 2.50e+03
        pdb=" O   GLY A1447 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   SER A1448 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A1817 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.06e+00
        pdb=" N   PRO A1818 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A1818 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A1818 "    0.031 5.00e-02 4.00e+02
  ... (remaining 2084 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1149
        2.74 -     3.28: 11536
        3.28 -     3.82: 19044
        3.82 -     4.36: 20407
        4.36 -     4.90: 36089
  Nonbonded interactions: 88225
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 887 "
            pdb=" OG1 THR A 891 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   SER A 603 "
            pdb=" OG1 THR A 607 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OG1 THR A1040 "
            pdb=" OE1 GLU A1041 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   ILE A 648 "
            pdb=" OG  SER A 652 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   ASP A 374 "
            pdb=" NH1 ARG A 376 "
     model   vdw
     2.324 3.120
  ... (remaining 88220 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  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:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     28.050
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
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      :  0.003   0.059  12239  Z= 0.168
  Angle     :  0.618  11.363  16620  Z= 0.350
  Chirality :  0.042   0.229   1845
  Planarity :  0.005   0.109   2087
  Dihedral  : 16.842  89.891   4366
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.64 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 25.02 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.22), residues: 1471
  helix:  1.34 (0.18), residues: 847
  sheet:  0.06 (0.82), residues: 37
  loop : -1.75 (0.25), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1474 
 HIS   0.006   0.001   HIS A1838 
 PHE   0.024   0.001   PHE A 685 
 TYR   0.014   0.001   TYR A1292 
 ARG   0.003   0.000   ARG A1332 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14199 (  641)
  hydrogen bonds       : angle       4.91448 ( 1896)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.76118 (    2)
  covalent geometry    : bond        0.00343 (12238)
  covalent geometry    : angle       0.61765 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 119
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  777 TYR cc_start: 0.5355 (OUTLIER) cc_final: 0.3584 (t80)
REVERT: A 1597 ASN cc_start: 0.8165 (t0) cc_final: 0.7913 (t0)
  outliers start: 4
  outliers final: 1
  residues processed: 122
  average time/residue: 0.2702
  time to fit residues: 47.2855
Evaluate side-chains
  118 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue 1148 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    2.9990
   chunk 112 optimal weight:    0.4980
   chunk 62 optimal weight:   20.0000
   chunk 38 optimal weight:    0.5980
   chunk 75 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 116 optimal weight:    0.8980
   chunk 44 optimal weight:    0.3980
   chunk 70 optimal weight:   30.0000
   chunk 86 optimal weight:    0.6980
   chunk 134 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 HIS
A 771 HIS
A 848 HIS
A1748 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.225049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.179301 restraints weight = 13360.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.54
r_work: 0.3482 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12239  Z= 0.130
  Angle     :  0.534   8.737  16620  Z= 0.279
  Chirality :  0.039   0.144   1845
  Planarity :  0.004   0.066   2087
  Dihedral  :  4.415  45.983   1632
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 24.54 %
    Favored  : 72.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.23), residues: 1471
  helix:  1.54 (0.18), residues: 856
  sheet: -0.41 (0.88), residues: 34
  loop : -1.72 (0.25), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 456 
 HIS   0.005   0.001   HIS A1748 
 PHE   0.015   0.001   PHE A 685 
 TYR   0.012   0.001   TYR A1800 
 ARG   0.002   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06487 (  641)
  hydrogen bonds       : angle       4.37379 ( 1896)
  SS BOND              : bond        0.00084 (    1)
  SS BOND              : angle       0.69465 (    2)
  covalent geometry    : bond        0.00250 (12238)
  covalent geometry    : angle       0.53370 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 1.228 
Fit side-chains
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.7865 (mm110) cc_final: 0.7297 (mt0)
REVERT: A  430 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7534 (p)
REVERT: A  713 ILE cc_start: 0.3698 (OUTLIER) cc_final: 0.3020 (tp)
REVERT: A  716 LEU cc_start: 0.1392 (OUTLIER) cc_final: 0.0907 (pp)
REVERT: A  777 TYR cc_start: 0.4684 (OUTLIER) cc_final: 0.2645 (t80)
REVERT: A 1597 ASN cc_start: 0.8510 (t0) cc_final: 0.8174 (t0)
  outliers start: 31
  outliers final: 15
  residues processed: 152
  average time/residue: 0.2385
  time to fit residues: 52.7418
Evaluate side-chains
  137 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 VAL
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue  949 THR
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1192 HIS
Chi-restraints excluded: chain A residue 1204 MET
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1586 THR
Chi-restraints excluded: chain A residue 1654 HIS
Chi-restraints excluded: chain A residue 1689 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 82 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9980
   chunk 135 optimal weight:    0.5980
   chunk 121 optimal weight:    9.9990
   chunk 32 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9990
   chunk 122 optimal weight:    8.9990
   chunk 115 optimal weight:    0.8980
   chunk 104 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 721 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.223461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.177857 restraints weight = 13567.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.4053 rms_B_bonded: 3.54
r_work: 0.3455 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.1007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12239  Z= 0.133
  Angle     :  0.528   8.660  16620  Z= 0.276
  Chirality :  0.039   0.133   1845
  Planarity :  0.004   0.054   2087
  Dihedral  :  4.255  48.561   1632
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 23.34 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.23), residues: 1471
  helix:  1.65 (0.18), residues: 855
  sheet: -0.16 (0.89), residues: 32
  loop : -1.65 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 625 
 HIS   0.002   0.001   HIS A1748 
 PHE   0.016   0.001   PHE A 685 
 TYR   0.013   0.001   TYR A1276 
 ARG   0.004   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06623 (  641)
  hydrogen bonds       : angle       4.29314 ( 1896)
  SS BOND              : bond        0.00121 (    1)
  SS BOND              : angle       0.51143 (    2)
  covalent geometry    : bond        0.00268 (12238)
  covalent geometry    : angle       0.52836 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 120
  time to evaluate  : 1.292 
Fit side-chains
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.7921 (mm110) cc_final: 0.7331 (mt0)
REVERT: A  620 MET cc_start: 0.7096 (tpt) cc_final: 0.6810 (mmt)
REVERT: A  713 ILE cc_start: 0.3658 (OUTLIER) cc_final: 0.3013 (tp)
REVERT: A  716 LEU cc_start: 0.1342 (OUTLIER) cc_final: 0.0861 (pp)
REVERT: A  777 TYR cc_start: 0.4790 (OUTLIER) cc_final: 0.2726 (t80)
REVERT: A 1571 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7299 (m-80)
REVERT: A 1589 LYS cc_start: 0.3634 (tppt) cc_final: 0.2836 (tptp)
REVERT: A 1597 ASN cc_start: 0.8411 (t0) cc_final: 0.8075 (t0)
REVERT: A 1603 ILE cc_start: 0.7976 (OUTLIER) cc_final: 0.7733 (tt)
  outliers start: 43
  outliers final: 18
  residues processed: 156
  average time/residue: 0.2412
  time to fit residues: 54.6084
Evaluate side-chains
  139 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 1.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue  949 THR
Chi-restraints excluded: chain A residue 1028 LEU
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1204 MET
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1571 TYR
Chi-restraints excluded: chain A residue 1586 THR
Chi-restraints excluded: chain A residue 1603 ILE
Chi-restraints excluded: chain A residue 1655 ILE
Chi-restraints excluded: chain A residue 1689 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 127 optimal weight:    4.9990
   chunk 122 optimal weight:    9.9990
   chunk 135 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.222813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.175776 restraints weight = 13354.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.4034 rms_B_bonded: 3.68
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12239  Z= 0.138
  Angle     :  0.544   8.768  16620  Z= 0.283
  Chirality :  0.040   0.233   1845
  Planarity :  0.004   0.050   2087
  Dihedral  :  4.214  49.262   1632
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 24.06 %
    Favored  : 72.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.23), residues: 1471
  helix:  1.68 (0.18), residues: 854
  sheet: -0.64 (0.90), residues: 34
  loop : -1.57 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 224 
 HIS   0.002   0.001   HIS A1323 
 PHE   0.016   0.001   PHE A 517 
 TYR   0.014   0.001   TYR A1276 
 ARG   0.004   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06698 (  641)
  hydrogen bonds       : angle       4.28982 ( 1896)
  SS BOND              : bond        0.00141 (    1)
  SS BOND              : angle       0.42354 (    2)
  covalent geometry    : bond        0.00286 (12238)
  covalent geometry    : angle       0.54352 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 117
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
REVERT: A  620 MET cc_start: 0.6474 (tpt) cc_final: 0.6213 (mmt)
REVERT: A  713 ILE cc_start: 0.3857 (OUTLIER) cc_final: 0.3234 (tp)
REVERT: A  716 LEU cc_start: 0.1937 (OUTLIER) cc_final: 0.1226 (pp)
REVERT: A  777 TYR cc_start: 0.5169 (OUTLIER) cc_final: 0.3294 (t80)
REVERT: A 1571 TYR cc_start: 0.7685 (OUTLIER) cc_final: 0.7445 (m-80)
REVERT: A 1589 LYS cc_start: 0.3888 (tppt) cc_final: 0.2904 (tptp)
REVERT: A 1603 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7606 (tt)
  outliers start: 38
  outliers final: 22
  residues processed: 150
  average time/residue: 0.2576
  time to fit residues: 55.4783
Evaluate side-chains
  142 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue  949 THR
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1028 LEU
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1204 MET
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1571 TYR
Chi-restraints excluded: chain A residue 1586 THR
Chi-restraints excluded: chain A residue 1603 ILE
Chi-restraints excluded: chain A residue 1694 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 36 optimal weight:    0.4980
   chunk 14 optimal weight:    0.4980
   chunk 58 optimal weight:    7.9990
   chunk 107 optimal weight:    0.7980
   chunk 23 optimal weight:    0.1980
   chunk 129 optimal weight:    8.9990
   chunk 128 optimal weight:    3.9990
   chunk 139 optimal weight:    7.9990
   chunk 54 optimal weight:   10.0000
   chunk 62 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.223144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.174761 restraints weight = 13384.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.4023 rms_B_bonded: 3.58
r_work: 0.3451 rms_B_bonded: 4.91 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12239  Z= 0.133
  Angle     :  0.534   8.683  16620  Z= 0.278
  Chirality :  0.039   0.173   1845
  Planarity :  0.004   0.050   2087
  Dihedral  :  4.145  50.785   1632
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 23.90 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.23), residues: 1471
  helix:  1.70 (0.18), residues: 859
  sheet: -0.28 (0.92), residues: 32
  loop : -1.53 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 625 
 HIS   0.004   0.000   HIS A1748 
 PHE   0.015   0.001   PHE A 517 
 TYR   0.013   0.001   TYR A1276 
 ARG   0.004   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06507 (  641)
  hydrogen bonds       : angle       4.23962 ( 1896)
  SS BOND              : bond        0.00096 (    1)
  SS BOND              : angle       0.49737 (    2)
  covalent geometry    : bond        0.00274 (12238)
  covalent geometry    : angle       0.53391 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 121
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6834 (p90)
REVERT: A  620 MET cc_start: 0.7156 (tpt) cc_final: 0.6899 (mmt)
REVERT: A  716 LEU cc_start: 0.0837 (OUTLIER) cc_final: 0.0365 (pp)
REVERT: A  777 TYR cc_start: 0.4243 (OUTLIER) cc_final: 0.2236 (t80)
REVERT: A 1028 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8318 (tt)
REVERT: A 1571 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.7348 (m-80)
REVERT: A 1589 LYS cc_start: 0.3523 (tppt) cc_final: 0.2697 (tppt)
  outliers start: 37
  outliers final: 23
  residues processed: 153
  average time/residue: 0.2471
  time to fit residues: 55.0581
Evaluate side-chains
  144 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  443 ARG
Chi-restraints excluded: chain A residue  475 TYR
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue  949 THR
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1028 LEU
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1204 MET
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1571 TYR
Chi-restraints excluded: chain A residue 1586 THR
Chi-restraints excluded: chain A residue 1689 CYS
Chi-restraints excluded: chain A residue 1694 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 126 optimal weight:    0.0010
   chunk 90 optimal weight:    0.6980
   chunk 135 optimal weight:    1.9990
   chunk 101 optimal weight:    0.5980
   chunk 80 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 35 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 26 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.224536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.176858 restraints weight = 13484.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.4045 rms_B_bonded: 3.68
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7031
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12239  Z= 0.122
  Angle     :  0.520   8.269  16620  Z= 0.268
  Chirality :  0.039   0.152   1845
  Planarity :  0.004   0.049   2087
  Dihedral  :  4.057  51.316   1632
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 23.74 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.23), residues: 1471
  helix:  1.79 (0.18), residues: 865
  sheet: -0.64 (0.91), residues: 34
  loop : -1.54 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 224 
 HIS   0.004   0.000   HIS A1748 
 PHE   0.013   0.001   PHE A 517 
 TYR   0.011   0.001   TYR A1276 
 ARG   0.004   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05969 (  641)
  hydrogen bonds       : angle       4.17244 ( 1896)
  SS BOND              : bond        0.00085 (    1)
  SS BOND              : angle       0.51430 (    2)
  covalent geometry    : bond        0.00243 (12238)
  covalent geometry    : angle       0.51988 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 118
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.6600 (p90)
REVERT: A  620 MET cc_start: 0.6369 (tpt) cc_final: 0.6135 (mmt)
REVERT: A  716 LEU cc_start: 0.1591 (OUTLIER) cc_final: 0.0884 (pp)
REVERT: A  722 ILE cc_start: 0.5050 (OUTLIER) cc_final: 0.4780 (tp)
REVERT: A  777 TYR cc_start: 0.4980 (OUTLIER) cc_final: 0.3135 (t80)
REVERT: A 1028 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8097 (tt)
REVERT: A 1204 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8665 (mmm)
REVERT: A 1589 LYS cc_start: 0.3433 (tppt) cc_final: 0.2841 (tppt)
REVERT: A 1597 ASN cc_start: 0.8127 (t0) cc_final: 0.7809 (t0)
REVERT: A 1603 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7584 (tt)
  outliers start: 40
  outliers final: 24
  residues processed: 149
  average time/residue: 0.2666
  time to fit residues: 56.6836
Evaluate side-chains
  146 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 1.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  443 ARG
Chi-restraints excluded: chain A residue  475 TYR
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  722 ILE
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue  949 THR
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1028 LEU
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1204 MET
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1368 ILE
Chi-restraints excluded: chain A residue 1562 MET
Chi-restraints excluded: chain A residue 1586 THR
Chi-restraints excluded: chain A residue 1603 ILE
Chi-restraints excluded: chain A residue 1689 CYS
Chi-restraints excluded: chain A residue 1694 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 22 optimal weight:    0.6980
   chunk 85 optimal weight:    0.5980
   chunk 87 optimal weight:    1.9990
   chunk 115 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 141 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 128 optimal weight:    7.9990
   chunk 117 optimal weight:    0.6980
   chunk 119 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.222455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.148074 restraints weight = 13227.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.69
r_work: 0.3515 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
moved from start:          0.1657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12239  Z= 0.130
  Angle     :  0.530   7.981  16620  Z= 0.275
  Chirality :  0.039   0.148   1845
  Planarity :  0.004   0.049   2087
  Dihedral  :  4.071  52.468   1632
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 24.54 %
    Favored  : 72.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.23), residues: 1471
  helix:  1.77 (0.18), residues: 866
  sheet: -0.04 (0.93), residues: 32
  loop : -1.54 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 224 
 HIS   0.005   0.001   HIS A1748 
 PHE   0.015   0.001   PHE A 517 
 TYR   0.013   0.001   TYR A1276 
 ARG   0.004   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06326 (  641)
  hydrogen bonds       : angle       4.17733 ( 1896)
  SS BOND              : bond        0.00106 (    1)
  SS BOND              : angle       0.44089 (    2)
  covalent geometry    : bond        0.00268 (12238)
  covalent geometry    : angle       0.53018 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
REVERT: A  475 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6587 (p90)
REVERT: A  620 MET cc_start: 0.6888 (tpt) cc_final: 0.6656 (mmt)
REVERT: A  663 TRP cc_start: 0.7217 (OUTLIER) cc_final: 0.6408 (m-10)
REVERT: A  716 LEU cc_start: 0.0519 (OUTLIER) cc_final: 0.0092 (pp)
REVERT: A  722 ILE cc_start: 0.4960 (OUTLIER) cc_final: 0.4564 (tp)
REVERT: A  777 TYR cc_start: 0.3911 (OUTLIER) cc_final: 0.2091 (t80)
REVERT: A 1204 MET cc_start: 0.9222 (mtp) cc_final: 0.8967 (mmm)
REVERT: A 1571 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6958 (m-80)
REVERT: A 1589 LYS cc_start: 0.2522 (tppt) cc_final: 0.1863 (tppt)
REVERT: A 1603 ILE cc_start: 0.7865 (OUTLIER) cc_final: 0.7641 (tt)
  outliers start: 39
  outliers final: 25
  residues processed: 147
  average time/residue: 0.2676
  time to fit residues: 57.1482
Evaluate side-chains
  145 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  443 ARG
Chi-restraints excluded: chain A residue  458 MET
Chi-restraints excluded: chain A residue  475 TYR
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain A residue  663 TRP
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  722 ILE
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue  949 THR
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1028 LEU
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1562 MET
Chi-restraints excluded: chain A residue 1571 TYR
Chi-restraints excluded: chain A residue 1586 THR
Chi-restraints excluded: chain A residue 1603 ILE
Chi-restraints excluded: chain A residue 1689 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 139 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0270
   chunk 80 optimal weight:    0.1980
   chunk 20 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.5038

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.225221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 82)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.153263 restraints weight = 13310.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3751 rms_B_bonded: 2.71
r_work: 0.3542 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12239  Z= 0.117
  Angle     :  0.517   8.301  16620  Z= 0.264
  Chirality :  0.038   0.155   1845
  Planarity :  0.004   0.049   2087
  Dihedral  :  3.976  53.035   1632
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 24.94 %
    Favored  : 72.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.23), residues: 1471
  helix:  1.90 (0.18), residues: 867
  sheet: -0.44 (0.93), residues: 34
  loop : -1.52 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 456 
 HIS   0.004   0.000   HIS A1748 
 PHE   0.011   0.001   PHE A 517 
 TYR   0.011   0.001   TYR A1800 
 ARG   0.003   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05540 (  641)
  hydrogen bonds       : angle       4.09758 ( 1896)
  SS BOND              : bond        0.00066 (    1)
  SS BOND              : angle       0.52606 (    2)
  covalent geometry    : bond        0.00232 (12238)
  covalent geometry    : angle       0.51682 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 118
  time to evaluate  : 1.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 TYR cc_start: 0.6936 (OUTLIER) cc_final: 0.6516 (p90)
REVERT: A  620 MET cc_start: 0.6734 (tpt) cc_final: 0.6520 (mmt)
REVERT: A  685 PHE cc_start: 0.6751 (OUTLIER) cc_final: 0.6143 (t80)
REVERT: A  713 ILE cc_start: 0.3990 (OUTLIER) cc_final: 0.3517 (tp)
REVERT: A  716 LEU cc_start: 0.0640 (OUTLIER) cc_final: 0.0217 (pp)
REVERT: A  722 ILE cc_start: 0.4892 (OUTLIER) cc_final: 0.4497 (tp)
REVERT: A  777 TYR cc_start: 0.3798 (OUTLIER) cc_final: 0.3306 (t80)
REVERT: A  839 MET cc_start: 0.9081 (ptm) cc_final: 0.8846 (ttp)
REVERT: A 1028 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8189 (tt)
REVERT: A 1204 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8959 (mmm)
REVERT: A 1571 TYR cc_start: 0.7657 (OUTLIER) cc_final: 0.6544 (m-80)
REVERT: A 1589 LYS cc_start: 0.2379 (tppt) cc_final: 0.1664 (tppt)
  outliers start: 35
  outliers final: 20
  residues processed: 145
  average time/residue: 0.2541
  time to fit residues: 53.5215
Evaluate side-chains
  144 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  443 ARG
Chi-restraints excluded: chain A residue  475 TYR
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  722 ILE
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue  949 THR
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1028 LEU
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1204 MET
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1571 TYR
Chi-restraints excluded: chain A residue 1586 THR
Chi-restraints excluded: chain A residue 1689 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   chunk 64 optimal weight:   20.0000
   chunk 76 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0070
   chunk 116 optimal weight:    1.9990
   chunk 8 optimal weight:    0.2980
   chunk 87 optimal weight:    0.8980
   chunk 126 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.8200

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

Flipped N/Q/H residues before XYZ refinement:
** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4466 r_free = 0.4466 target = 0.222308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.162414 restraints weight = 13341.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3807 rms_B_bonded: 6.07
r_work: 0.3462 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.1903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12239  Z= 0.133
  Angle     :  0.541   8.694  16620  Z= 0.279
  Chirality :  0.039   0.155   1845
  Planarity :  0.004   0.049   2087
  Dihedral  :  4.037  54.456   1632
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 24.86 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.82 (0.23), residues: 1471
  helix:  1.82 (0.18), residues: 867
  sheet:  0.04 (0.94), residues: 32
  loop : -1.52 (0.26), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 224 
 HIS   0.004   0.000   HIS A1748 
 PHE   0.016   0.001   PHE A 517 
 TYR   0.014   0.001   TYR A1276 
 ARG   0.003   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06406 (  641)
  hydrogen bonds       : angle       4.16313 ( 1896)
  SS BOND              : bond        0.00130 (    1)
  SS BOND              : angle       0.36566 (    2)
  covalent geometry    : bond        0.00276 (12238)
  covalent geometry    : angle       0.54115 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 117
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6571 (p90)
REVERT: A  620 MET cc_start: 0.6964 (tpt) cc_final: 0.6754 (mmt)
REVERT: A  663 TRP cc_start: 0.7134 (OUTLIER) cc_final: 0.6353 (m-10)
REVERT: A  713 ILE cc_start: 0.3802 (OUTLIER) cc_final: 0.3344 (tp)
REVERT: A  716 LEU cc_start: 0.0559 (OUTLIER) cc_final: 0.0185 (pp)
REVERT: A  777 TYR cc_start: 0.3751 (OUTLIER) cc_final: 0.3108 (t80)
REVERT: A 1204 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8941 (mmm)
REVERT: A 1308 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7107 (mm)
REVERT: A 1571 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6485 (m-80)
REVERT: A 1589 LYS cc_start: 0.2506 (tppt) cc_final: 0.2276 (tppt)
REVERT: A 1597 ASN cc_start: 0.8302 (t0) cc_final: 0.8004 (t0)
  outliers start: 39
  outliers final: 25
  residues processed: 150
  average time/residue: 0.2577
  time to fit residues: 56.3273
Evaluate side-chains
  145 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 112
  time to evaluate  : 1.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  384 HIS
Chi-restraints excluded: chain A residue  475 TYR
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain A residue  663 TRP
Chi-restraints excluded: chain A residue  669 CYS
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue  949 THR
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1028 LEU
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1192 HIS
Chi-restraints excluded: chain A residue 1204 MET
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1341 VAL
Chi-restraints excluded: chain A residue 1571 TYR
Chi-restraints excluded: chain A residue 1586 THR
Chi-restraints excluded: chain A residue 1689 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0970
   chunk 106 optimal weight:    1.9990
   chunk 31 optimal weight:    6.9990
   chunk 132 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9980
   chunk 39 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 55 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 115 optimal weight:    3.9990
   overall best weight:    0.9980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.220333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.147121 restraints weight = 13089.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.89
r_work: 0.3490 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12239  Z= 0.143
  Angle     :  0.556   9.062  16620  Z= 0.288
  Chirality :  0.040   0.145   1845
  Planarity :  0.005   0.098   2087
  Dihedral  :  4.148  56.220   1632
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 25.58 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.23), residues: 1471
  helix:  1.79 (0.18), residues: 864
  sheet: -0.43 (0.88), residues: 39
  loop : -1.52 (0.26), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 456 
 HIS   0.004   0.001   HIS A1748 
 PHE   0.019   0.001   PHE A 517 
 TYR   0.015   0.001   TYR A1276 
 ARG   0.003   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06878 (  641)
  hydrogen bonds       : angle       4.23984 ( 1896)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       0.41247 (    2)
  covalent geometry    : bond        0.00303 (12238)
  covalent geometry    : angle       0.55570 (16618)

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

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

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2942 Ramachandran restraints generated.
    1471 Oldfield, 0 Emsley, 1471 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 111
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  475 TYR cc_start: 0.7143 (OUTLIER) cc_final: 0.6699 (p90)
REVERT: A  620 MET cc_start: 0.7048 (tpt) cc_final: 0.6804 (mmt)
REVERT: A  663 TRP cc_start: 0.7172 (OUTLIER) cc_final: 0.6550 (m-10)
REVERT: A  713 ILE cc_start: 0.3879 (OUTLIER) cc_final: 0.3389 (tp)
REVERT: A  716 LEU cc_start: 0.0537 (OUTLIER) cc_final: 0.0158 (pp)
REVERT: A  777 TYR cc_start: 0.3611 (OUTLIER) cc_final: 0.2789 (t80)
REVERT: A 1058 ILE cc_start: 0.6818 (mm) cc_final: 0.6280 (mm)
REVERT: A 1204 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8934 (mmm)
REVERT: A 1308 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7139 (mm)
REVERT: A 1571 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.6493 (m-80)
REVERT: A 1589 LYS cc_start: 0.2298 (tppt) cc_final: 0.2054 (tppt)
REVERT: A 1597 ASN cc_start: 0.8424 (t0) cc_final: 0.8099 (t0)
  outliers start: 34
  outliers final: 23
  residues processed: 140
  average time/residue: 0.2554
  time to fit residues: 52.1046
Evaluate side-chains
  139 residues out of total 1307 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 108
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 MET
Chi-restraints excluded: chain A residue  311 CYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  384 HIS
Chi-restraints excluded: chain A residue  387 ILE
Chi-restraints excluded: chain A residue  475 TYR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain A residue  597 THR
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  650 ILE
Chi-restraints excluded: chain A residue  663 TRP
Chi-restraints excluded: chain A residue  669 CYS
Chi-restraints excluded: chain A residue  685 PHE
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  703 PHE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  749 LEU
Chi-restraints excluded: chain A residue  777 TYR
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1028 LEU
Chi-restraints excluded: chain A residue 1088 HIS
Chi-restraints excluded: chain A residue 1148 VAL
Chi-restraints excluded: chain A residue 1204 MET
Chi-restraints excluded: chain A residue 1268 GLU
Chi-restraints excluded: chain A residue 1308 LEU
Chi-restraints excluded: chain A residue 1341 VAL
Chi-restraints excluded: chain A residue 1571 TYR
Chi-restraints excluded: chain A residue 1586 THR
Chi-restraints excluded: chain A residue 1689 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 85 optimal weight:    6.9990
   chunk 135 optimal weight:    4.9990
   chunk 84 optimal weight:    0.0970
   chunk 59 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0570
   chunk 114 optimal weight:    0.0070
   chunk 28 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.5916

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.223856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.164573 restraints weight = 13328.738|
|-----------------------------------------------------------------------------|
r_work (start): 0.3853 rms_B_bonded: 6.35
r_work: 0.3488 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  12239  Z= 0.123
  Angle     :  0.526   8.966  16620  Z= 0.271
  Chirality :  0.039   0.151   1845
  Planarity :  0.004   0.082   2087
  Dihedral  :  4.029  56.978   1632
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 25.42 %
    Favored  : 72.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.23), residues: 1471
  helix:  1.89 (0.18), residues: 868
  sheet: -0.39 (0.94), residues: 34
  loop : -1.48 (0.26), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 456 
 HIS   0.004   0.000   HIS A1748 
 PHE   0.022   0.001   PHE A 238 
 TYR   0.012   0.001   TYR A1276 
 ARG   0.003   0.000   ARG A 376 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05877 (  641)
  hydrogen bonds       : angle       4.12688 ( 1896)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       0.43745 (    2)
  covalent geometry    : bond        0.00245 (12238)
  covalent geometry    : angle       0.52634 (16618)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6982.94 seconds
wall clock time: 122 minutes 8.97 seconds (7328.97 seconds total)