Starting phenix.real_space_refine
on Tue May 13 05:57:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wi0_37554/05_2025/8wi0_37554.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wi0_37554/05_2025/8wi0_37554.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wi0_37554/05_2025/8wi0_37554.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wi0_37554/05_2025/8wi0_37554.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wi0_37554/05_2025/8wi0_37554.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wi0_37554/05_2025/8wi0_37554.cif"
  }
  resolution = 2.93
  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=   0.001 sd=   0.054
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      59      5.16       5
     C    6233      2.51       5
     N    1657      2.21       5
     O    1766      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9716
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1220, 9580
          Classifications: {'peptide': 1220}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 35, 'TRANS': 1182}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 136
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 136
          Classifications: {'peptide': 19}
          Link IDs: {'TRANS': 18}
  Time building chain proxies: 5.70, per 1000 atoms: 0.59
  Number of scatterers: 9716
  At special positions: 0
  Unit cell: (75.04, 112.56, 154.368, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      59     16.00
     P       1     15.00
     O    1766      8.00
     N    1657      7.00
     C    6233      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.52
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2332

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 8 sheets defined
      70.1% alpha, 7.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 105 through 112
    Processing helix  chain 'A' and resid 112 through 126
    Processing helix  chain 'A' and resid 137 through 140
    Processing helix  chain 'A' and resid 141 through 161
      removed outlier: 3.539A  pdb=" N   ASN A 145 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 209
      removed outlier: 5.427A  pdb=" N   THR A 177 " --> pdb=" O   ILE A 173 " (cutoff:3.500A)
      removed outlier: 6.163A  pdb=" N   ARG A 178 " --> pdb=" O   PHE A 174 " (cutoff:3.500A)
      Proline residue:  A 197  - end of helix
    Processing helix  chain 'A' and resid 214 through 263
      removed outlier: 3.539A  pdb=" N   SER A 218 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU A 219 " --> pdb=" O   LEU A 215 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LEU A 220 " --> pdb=" O   GLN A 216 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 282
      removed outlier: 3.556A  pdb=" N   CYS A 280 " --> pdb=" O   LEU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 298
    Processing helix  chain 'A' and resid 299 through 316
      removed outlier: 4.412A  pdb=" N   VAL A 303 " --> pdb=" O   GLY A 299 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ALA A 304 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 364
      removed outlier: 3.991A  pdb=" N   GLY A 322 " --> pdb=" O   THR A 318 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE A 326 " --> pdb=" O   GLY A 322 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE A 327 " --> pdb=" O   SER A 323 " (cutoff:3.500A)
      Proline residue:  A 331  - end of helix
      removed outlier: 3.623A  pdb=" N   LYS A 346 " --> pdb=" O   TYR A 342 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ALA A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 372
    Processing helix  chain 'A' and resid 373 through 402
      removed outlier: 3.753A  pdb=" N   PHE A 377 " --> pdb=" O   TRP A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 424
      removed outlier: 4.382A  pdb=" N   ILE A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LEU A 424 " --> pdb=" O   VAL A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 472
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 600 through 610
    Processing helix  chain 'A' and resid 640 through 645
    Processing helix  chain 'A' and resid 650 through 661
    Processing helix  chain 'A' and resid 663 through 670
    Processing helix  chain 'A' and resid 672 through 676
    Processing helix  chain 'A' and resid 686 through 702
    Processing helix  chain 'A' and resid 716 through 728
    Processing helix  chain 'A' and resid 730 through 735
      removed outlier: 4.138A  pdb=" N   LYS A 733 " --> pdb=" O   LYS A 730 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   SER A 734 " --> pdb=" O   HIS A 731 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 750
      removed outlier: 3.810A  pdb=" N   TYR A 746 " --> pdb=" O   GLN A 743 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU A 747 " --> pdb=" O   LEU A 744 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   VAL A 748 " --> pdb=" O   GLN A 745 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   ASP A 749 " --> pdb=" O   TYR A 746 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 774
    Processing helix  chain 'A' and resid 775 through 786
    Processing helix  chain 'A' and resid 842 through 854
      removed outlier: 4.028A  pdb=" N   TYR A 846 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 887
      removed outlier: 3.842A  pdb=" N   GLY A 887 " --> pdb=" O   TRP A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 908
    Processing helix  chain 'A' and resid 910 through 956
    Processing helix  chain 'A' and resid 959 through 966
      removed outlier: 3.961A  pdb=" N   PHE A 963 " --> pdb=" O   PRO A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 1011
      removed outlier: 3.750A  pdb=" N   ILE A 971 " --> pdb=" O   PRO A 967 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ASP A 978 " --> pdb=" O   ARG A 974 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   MET A 979 " --> pdb=" O   PHE A 975 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASP A 980 " --> pdb=" O   SER A 976 " (cutoff:3.500A)
      Proline residue:  A 987  - end of helix
    Processing helix  chain 'A' and resid 1011 through 1046
      removed outlier: 3.974A  pdb=" N   LEU A1015 " --> pdb=" O   PHE A1011 " (cutoff:3.500A)
      Proline residue:  A1020  - end of helix
      removed outlier: 3.529A  pdb=" N   ILE A1036 " --> pdb=" O   SER A1032 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG A1037 " --> pdb=" O   ARG A1033 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   GLU A1038 " --> pdb=" O   VAL A1034 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU A1042 " --> pdb=" O   GLU A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1046 through 1059
      removed outlier: 3.935A  pdb=" N   PHE A1050 " --> pdb=" O   THR A1046 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1060 through 1067
    Processing helix  chain 'A' and resid 1071 through 1120
      Proline residue:  A1087  - end of helix
    Processing helix  chain 'A' and resid 1125 through 1139
    Processing helix  chain 'A' and resid 1141 through 1170
      removed outlier: 4.215A  pdb=" N   PHE A1145 " --> pdb=" O   GLY A1141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1232 through 1234
      No H-bonds generated for 'chain 'A' and resid 1232 through 1234'
    Processing helix  chain 'A' and resid 1235 through 1241
    Processing helix  chain 'A' and resid 1259 through 1261
      No H-bonds generated for 'chain 'A' and resid 1259 through 1261'
    Processing helix  chain 'A' and resid 1262 through 1268
    Processing helix  chain 'A' and resid 1284 through 1289
    Processing helix  chain 'A' and resid 1295 through 1306
    Processing helix  chain 'A' and resid 1308 through 1314
    Processing helix  chain 'A' and resid 1324 through 1328
    Processing helix  chain 'A' and resid 1331 through 1345
    Processing helix  chain 'A' and resid 1361 through 1376
    Processing helix  chain 'A' and resid 1387 through 1392
      removed outlier: 3.601A  pdb=" N   VAL A1391 " --> pdb=" O   ARG A1387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1416
      removed outlier: 3.536A  pdb=" N   SER A1416 " --> pdb=" O   SER A1412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1420 through 1435
    Processing helix  chain 'B' and resid 48 through 56
    Processing sheet with id=AA1, first strand: chain 'A' and resid 584 through 586
      removed outlier: 3.804A  pdb=" N   ILE A 490 " --> pdb=" O   ILE A 585 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   SER A 618 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 575 through 576
      removed outlier: 4.026A  pdb=" N   ALA A 498 " --> pdb=" O   THR A 613 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   THR A 613 " --> pdb=" O   ALA A 498 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 625 through 628
      removed outlier: 3.558A  pdb=" N   ILE A 707 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP A 709 " --> pdb=" O   VAL A 628 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   TYR A 706 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   VAL A 740 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   LEU A 708 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   VAL A 591 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   GLY A 592 " --> pdb=" O   ILE A 754 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   MET A 756 " --> pdb=" O   GLY A 592 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   CYS A 594 " --> pdb=" O   MET A 756 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   VAL A 753 " --> pdb=" O   ARG A 764 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   ARG A 764 " --> pdb=" O   VAL A 753 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   PHE A 755 " --> pdb=" O   THR A 762 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   THR A 762 " --> pdb=" O   PHE A 755 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 892 through 894
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1210 through 1213
      removed outlier: 5.951A  pdb=" N   LYS A1211 " --> pdb=" O   MET A1200 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   MET A1200 " --> pdb=" O   LYS A1211 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A1213 " --> pdb=" O   ALA A1198 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1210 through 1213
      removed outlier: 5.951A  pdb=" N   LYS A1211 " --> pdb=" O   MET A1200 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   MET A1200 " --> pdb=" O   LYS A1211 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   VAL A1213 " --> pdb=" O   ALA A1198 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   GLU A1196 " --> pdb=" O   CYS A1250 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   CYS A1250 " --> pdb=" O   GLU A1196 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   ALA A1198 " --> pdb=" O   GLY A1248 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   GLY A1248 " --> pdb=" O   ALA A1198 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1271 through 1273
      removed outlier: 3.751A  pdb=" N   SER A1271 " --> pdb=" O   ILE A1350 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   LEU A1351 " --> pdb=" O   LEU A1382 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   ILE A1384 " --> pdb=" O   LEU A1351 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   LEU A1353 " --> pdb=" O   ILE A1384 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   ARG A1396 " --> pdb=" O   LYS A1222 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLY A1224 " --> pdb=" O   ARG A1396 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LEU A1400 " --> pdb=" O   VAL A1226 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASP A1409 " --> pdb=" O   ILE A1397 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL A1399 " --> pdb=" O   GLU A1407 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLU A1407 " --> pdb=" O   VAL A1399 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1282 through 1283

    646 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: 3.46

  Time building geometry restraints manager: 2.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1901
        1.33 -     1.45: 2289
        1.45 -     1.57: 5609
        1.57 -     1.69: 2
        1.69 -     1.81: 99
  Bond restraints: 9900
  Sorted by residual:
  bond pdb=" O3P SEP B  60 "
       pdb=" P   SEP B  60 "
    ideal  model  delta    sigma   weight residual
    1.610  1.510  0.100 2.00e-02 2.50e+03 2.51e+01
  bond pdb=" O1P SEP B  60 "
       pdb=" P   SEP B  60 "
    ideal  model  delta    sigma   weight residual
    1.610  1.512  0.098 2.00e-02 2.50e+03 2.41e+01
  bond pdb=" O2P SEP B  60 "
       pdb=" P   SEP B  60 "
    ideal  model  delta    sigma   weight residual
    1.610  1.518  0.092 2.00e-02 2.50e+03 2.10e+01
  bond pdb=" CB  PRO A 162 "
       pdb=" CG  PRO A 162 "
    ideal  model  delta    sigma   weight residual
    1.492  1.594 -0.102 5.00e-02 4.00e+02 4.17e+00
  bond pdb=" CA  THR A 450 "
       pdb=" C   THR A 450 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 1.23e-02 6.61e+03 3.65e+00
  ... (remaining 9895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 13043
        1.73 -     3.47: 303
        3.47 -     5.20: 46
        5.20 -     6.93: 7
        6.93 -     8.66: 2
  Bond angle restraints: 13401
  Sorted by residual:
  angle pdb=" N   ILE A 643 "
        pdb=" CA  ILE A 643 "
        pdb=" C   ILE A 643 "
      ideal   model   delta    sigma   weight residual
     112.96  107.59    5.37 1.00e+00 1.00e+00 2.89e+01
  angle pdb=" N   THR A 450 "
        pdb=" CA  THR A 450 "
        pdb=" C   THR A 450 "
      ideal   model   delta    sigma   weight residual
     112.75  119.82   -7.07 1.36e+00 5.41e-01 2.70e+01
  angle pdb=" N   GLY A1009 "
        pdb=" CA  GLY A1009 "
        pdb=" C   GLY A1009 "
      ideal   model   delta    sigma   weight residual
     114.16  109.74    4.42 1.21e+00 6.83e-01 1.33e+01
  angle pdb=" N   LEU A 273 "
        pdb=" CA  LEU A 273 "
        pdb=" C   LEU A 273 "
      ideal   model   delta    sigma   weight residual
     113.12  108.90    4.22 1.25e+00 6.40e-01 1.14e+01
  angle pdb=" N   GLY A 319 "
        pdb=" CA  GLY A 319 "
        pdb=" C   GLY A 319 "
      ideal   model   delta    sigma   weight residual
     114.66  110.94    3.72 1.24e+00 6.50e-01 8.99e+00
  ... (remaining 13396 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.42: 5065
       16.42 -    32.85: 653
       32.85 -    49.27: 180
       49.27 -    65.69: 40
       65.69 -    82.11: 14
  Dihedral angle restraints: 5952
    sinusoidal: 2355
      harmonic: 3597
  Sorted by residual:
  dihedral pdb=" CA  PHE A 625 "
           pdb=" C   PHE A 625 "
           pdb=" N   ALA A 626 "
           pdb=" CA  ALA A 626 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.64   19.36     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  GLY A 404 "
           pdb=" C   GLY A 404 "
           pdb=" N   VAL A 405 "
           pdb=" CA  VAL A 405 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.13  -17.87     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  ASP A1354 "
           pdb=" C   ASP A1354 "
           pdb=" N   GLU A1355 "
           pdb=" CA  GLU A1355 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.53   17.47     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 5949 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1059
       0.035 -    0.070: 378
       0.070 -    0.104: 93
       0.104 -    0.139: 36
       0.139 -    0.174: 4
  Chirality restraints: 1570
  Sorted by residual:
  chirality pdb=" CB  THR A 402 "
            pdb=" CA  THR A 402 "
            pdb=" OG1 THR A 402 "
            pdb=" CG2 THR A 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.17 2.00e-01 2.50e+01 7.57e-01
  chirality pdb=" CA  THR A 450 "
            pdb=" N   THR A 450 "
            pdb=" C   THR A 450 "
            pdb=" CB  THR A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.78e-01
  chirality pdb=" CA  ASN A 642 "
            pdb=" N   ASN A 642 "
            pdb=" C   ASN A 642 "
            pdb=" CB  ASN A 642 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.35e-01
  ... (remaining 1567 not shown)

  Planarity restraints: 1680
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  57 "    0.024 2.00e-02 2.50e+03   4.81e-02 2.31e+01
        pdb=" C   GLU B  57 "   -0.083 2.00e-02 2.50e+03
        pdb=" O   GLU B  57 "    0.031 2.00e-02 2.50e+03
        pdb=" N   GLY B  58 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 330 "    0.047 5.00e-02 4.00e+02   7.07e-02 8.00e+00
        pdb=" N   PRO A 331 "   -0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 855 "    0.041 5.00e-02 4.00e+02   6.30e-02 6.35e+00
        pdb=" N   PRO A 856 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 856 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 856 "    0.035 5.00e-02 4.00e+02
  ... (remaining 1677 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 287
        2.71 -     3.26: 9806
        3.26 -     3.80: 15853
        3.80 -     4.35: 19820
        4.35 -     4.90: 33612
  Nonbonded interactions: 79378
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 337 "
            pdb=" OD2 ASP B  48 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" O   ALA A1155 "
            pdb=" OG1 THR A1158 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   LEU A 128 "
            pdb=" NH2 ARG A1041 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" OG1 THR A 496 "
            pdb=" OE1 GLU A 616 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" OD1 ASN A 996 "
            pdb=" OG1 THR A1146 "
     model   vdw
     2.266 3.040
  ... (remaining 79373 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.130
  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:          0.360
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.750
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  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:10.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   9900  Z= 0.183
  Angle     :  0.639   8.664  13401  Z= 0.391
  Chirality :  0.040   0.174   1570
  Planarity :  0.005   0.071   1680
  Dihedral  : 16.326  82.114   3620
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  2.61 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 17.42 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.25), residues: 1228
  helix:  1.54 (0.18), residues: 805
  sheet:  0.13 (0.74), residues: 52
  loop : -1.21 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1097 
 HIS   0.004   0.001   HIS A1029 
 PHE   0.012   0.001   PHE A 398 
 TYR   0.013   0.001   TYR A 330 
 ARG   0.010   0.000   ARG A 957 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15835 (  645)
  hydrogen bonds       : angle       5.72931 ( 1896)
  covalent geometry    : bond        0.00350 ( 9900)
  covalent geometry    : angle       0.63921 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.967 
Fit side-chains
   revert: symmetry clash
  outliers start: 3
  outliers final: 2
  residues processed: 106
  average time/residue: 0.9968
  time to fit residues: 115.5228
Evaluate side-chains
  95 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  479 ILE
Chi-restraints excluded: chain B residue   61 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   chunk 51 optimal weight:    0.0070
   chunk 31 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:   10.0000
   chunk 96 optimal weight:   20.0000
   chunk 37 optimal weight:    0.6980
   chunk 58 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.8400

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

Flipped N/Q/H residues before XYZ refinement:
A 783 ASN
A1275 GLN
A1417 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.197409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.147760 restraints weight = 10253.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.26
r_work: 0.3342 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.0958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   9900  Z= 0.164
  Angle     :  0.550   8.221  13401  Z= 0.300
  Chirality :  0.041   0.162   1570
  Planarity :  0.005   0.065   1680
  Dihedral  :  5.049  61.228   1341
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.50 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.08 %
    Favored  : 79.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    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:  0.94 (0.24), residues: 1228
  helix:  1.52 (0.18), residues: 795
  sheet:  0.87 (0.73), residues: 51
  loop : -1.33 (0.31), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1097 
 HIS   0.004   0.001   HIS A1029 
 PHE   0.018   0.002   PHE A 434 
 TYR   0.013   0.001   TYR A 330 
 ARG   0.004   0.000   ARG A 953 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06995 (  645)
  hydrogen bonds       : angle       4.80480 ( 1896)
  covalent geometry    : bond        0.00346 ( 9900)
  covalent geometry    : angle       0.55031 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
REVERT: A  177 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.8130 (m)
REVERT: A  334 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7581 (mtm)
REVERT: A  338 ARG cc_start: 0.7987 (mpt90) cc_final: 0.7761 (mpt180)
REVERT: A  492 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.6740 (mpt)
REVERT: A 1238 MET cc_start: 0.8180 (OUTLIER) cc_final: 0.7829 (ttm)
  outliers start: 26
  outliers final: 12
  residues processed: 120
  average time/residue: 1.0039
  time to fit residues: 131.5361
Evaluate side-chains
  116 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  492 MET
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  971 ILE
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1045 ILE
Chi-restraints excluded: chain A residue 1048 SER
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1238 MET
Chi-restraints excluded: chain B residue   61 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0040
   chunk 61 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 50 optimal weight:   30.0000
   chunk 100 optimal weight:    4.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN
A1085 GLN
A1431 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.198045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.149317 restraints weight = 10297.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3593 rms_B_bonded: 2.37
r_work: 0.3257 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9900  Z= 0.144
  Angle     :  0.514   8.777  13401  Z= 0.278
  Chirality :  0.040   0.165   1570
  Planarity :  0.005   0.063   1680
  Dihedral  :  4.762  65.140   1339
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.55 %
    Favored  : 78.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.24), residues: 1228
  helix:  1.68 (0.18), residues: 797
  sheet:  1.05 (0.78), residues: 46
  loop : -1.12 (0.31), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A1029 
 PHE   0.014   0.001   PHE A 434 
 TYR   0.011   0.001   TYR A 330 
 ARG   0.003   0.000   ARG A 946 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06536 (  645)
  hydrogen bonds       : angle       4.57054 ( 1896)
  covalent geometry    : bond        0.00289 ( 9900)
  covalent geometry    : angle       0.51429 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 112
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
REVERT: A  334 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7672 (mtm)
REVERT: A  338 ARG cc_start: 0.8004 (mpt90) cc_final: 0.7720 (mpt180)
REVERT: A  631 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7595 (mp10)
REVERT: A  953 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7833 (ttp80)
REVERT: A 1016 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7817 (p)
REVERT: A 1095 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7890 (mpp)
REVERT: A 1166 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.6414 (t80)
REVERT: B   59 LEU cc_start: 0.7989 (OUTLIER) cc_final: 0.7746 (mp)
  outliers start: 36
  outliers final: 14
  residues processed: 138
  average time/residue: 1.0326
  time to fit residues: 154.7557
Evaluate side-chains
  125 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  841 VAL
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1045 ILE
Chi-restraints excluded: chain A residue 1048 SER
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1272 ILE
Chi-restraints excluded: chain A residue 1380 THR
Chi-restraints excluded: chain B residue   59 LEU
Chi-restraints excluded: chain B residue   61 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 55 optimal weight:    0.4980
   chunk 43 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 115 optimal weight:    4.9990
   chunk 91 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 108 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.196415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.147588 restraints weight = 10263.837|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 2.34
r_work: 0.3251 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9900  Z= 0.148
  Angle     :  0.522   7.576  13401  Z= 0.281
  Chirality :  0.041   0.270   1570
  Planarity :  0.004   0.062   1680
  Dihedral  :  4.693  66.242   1339
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 19.21 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.29 (0.24), residues: 1228
  helix:  1.75 (0.18), residues: 797
  sheet:  1.21 (0.74), residues: 51
  loop : -1.14 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 421 
 PHE   0.016   0.001   PHE A 434 
 TYR   0.011   0.001   TYR A 330 
 ARG   0.002   0.000   ARG A 946 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06573 (  645)
  hydrogen bonds       : angle       4.54587 ( 1896)
  covalent geometry    : bond        0.00307 ( 9900)
  covalent geometry    : angle       0.52228 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 115
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8646 (ptp)
REVERT: A  334 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7621 (mtm)
REVERT: A  338 ARG cc_start: 0.8016 (mpt90) cc_final: 0.7641 (mpt180)
REVERT: A  631 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7636 (mp10)
REVERT: A  953 ARG cc_start: 0.8172 (ttm-80) cc_final: 0.7796 (ttp80)
REVERT: A 1040 LYS cc_start: 0.8158 (tttm) cc_final: 0.7934 (tttp)
REVERT: A 1095 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.7841 (mpp)
REVERT: A 1166 TYR cc_start: 0.7812 (OUTLIER) cc_final: 0.6381 (t80)
REVERT: A 1221 GLU cc_start: 0.7476 (mt-10) cc_final: 0.7146 (mt-10)
REVERT: A 1238 MET cc_start: 0.8174 (tpp) cc_final: 0.7891 (ttm)
REVERT: B   59 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7747 (mp)
  outliers start: 38
  outliers final: 14
  residues processed: 141
  average time/residue: 1.0019
  time to fit residues: 154.3083
Evaluate side-chains
  132 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 112
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  841 VAL
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1048 SER
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1272 ILE
Chi-restraints excluded: chain A residue 1380 THR
Chi-restraints excluded: chain B residue   59 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 41 optimal weight:    7.9990
   chunk 118 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0970
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 481 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.195231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 131)---------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.144748 restraints weight = 10349.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 1.35
r_work: 0.3436 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3329 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.1871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9900  Z= 0.138
  Angle     :  0.498   7.586  13401  Z= 0.268
  Chirality :  0.040   0.145   1570
  Planarity :  0.004   0.061   1680
  Dihedral  :  4.430  71.422   1337
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.49 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.24), residues: 1228
  helix:  1.90 (0.18), residues: 796
  sheet:  1.22 (0.74), residues: 51
  loop : -1.15 (0.30), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1097 
 HIS   0.002   0.001   HIS A 421 
 PHE   0.014   0.001   PHE A 434 
 TYR   0.011   0.001   TYR A 330 
 ARG   0.002   0.000   ARG A 946 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06242 (  645)
  hydrogen bonds       : angle       4.41777 ( 1896)
  covalent geometry    : bond        0.00278 ( 9900)
  covalent geometry    : angle       0.49846 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 119
  time to evaluate  : 1.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  338 ARG cc_start: 0.8256 (mpt90) cc_final: 0.8002 (mpt180)
REVERT: A  360 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7822 (mt-10)
REVERT: A  438 THR cc_start: 0.8993 (m) cc_final: 0.8493 (p)
REVERT: A  631 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7759 (mp10)
REVERT: A  953 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7909 (ttp80)
REVERT: A  957 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6956 (ttp-170)
REVERT: A  980 ASP cc_start: 0.8672 (t70) cc_final: 0.8457 (t0)
REVERT: A 1040 LYS cc_start: 0.8286 (tttm) cc_final: 0.8053 (tttp)
REVERT: A 1095 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7783 (mpp)
REVERT: A 1238 MET cc_start: 0.8404 (tpp) cc_final: 0.8147 (ttm)
  outliers start: 36
  outliers final: 18
  residues processed: 142
  average time/residue: 1.0509
  time to fit residues: 163.3994
Evaluate side-chains
  129 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  877 THR
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  957 ARG
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1048 SER
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1154 GLU
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1272 ILE
Chi-restraints excluded: chain A residue 1351 LEU
Chi-restraints excluded: chain A residue 1380 THR
Chi-restraints excluded: chain A residue 1405 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 104 optimal weight:    6.9990
   chunk 49 optimal weight:    8.9990
   chunk 98 optimal weight:    1.9990
   chunk 39 optimal weight:    0.2980
   chunk 90 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 122 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 890 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.192096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.146332 restraints weight = 10252.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 2.49
r_work: 0.3178 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3052 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9900  Z= 0.171
  Angle     :  0.541   8.033  13401  Z= 0.292
  Chirality :  0.041   0.171   1570
  Planarity :  0.004   0.061   1680
  Dihedral  :  4.457  68.422   1337
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 19.96 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.24), residues: 1228
  helix:  1.77 (0.18), residues: 797
  sheet:  1.20 (0.73), residues: 51
  loop : -1.11 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 139 
 PHE   0.023   0.002   PHE A 434 
 TYR   0.011   0.001   TYR A 330 
 ARG   0.004   0.000   ARG A 664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07125 (  645)
  hydrogen bonds       : angle       4.53984 ( 1896)
  covalent geometry    : bond        0.00375 ( 9900)
  covalent geometry    : angle       0.54103 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 120
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8073 (pttm)
REVERT: A  491 GLU cc_start: 0.7452 (tt0) cc_final: 0.6674 (pp20)
REVERT: A  589 LYS cc_start: 0.7540 (mtpt) cc_final: 0.7180 (mmtm)
REVERT: A  631 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7707 (mp10)
REVERT: A  641 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7414 (m-30)
REVERT: A  953 ARG cc_start: 0.8216 (ttm-80) cc_final: 0.7575 (ttp80)
REVERT: A  957 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6952 (ttp-170)
REVERT: A  980 ASP cc_start: 0.8829 (t70) cc_final: 0.8569 (t0)
REVERT: A 1040 LYS cc_start: 0.8240 (tttm) cc_final: 0.7974 (tttp)
REVERT: A 1095 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7814 (mpp)
REVERT: A 1166 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6633 (t80)
REVERT: A 1221 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7549 (mt-10)
REVERT: A 1238 MET cc_start: 0.8188 (tpp) cc_final: 0.7895 (ttm)
REVERT: A 1381 MET cc_start: 0.6235 (OUTLIER) cc_final: 0.4545 (tmm)
  outliers start: 42
  outliers final: 19
  residues processed: 149
  average time/residue: 1.0262
  time to fit residues: 166.0505
Evaluate side-chains
  143 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 117
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LYS
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  314 ILE
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  613 THR
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain A residue  841 VAL
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue  957 ARG
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1048 SER
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1154 GLU
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1236 LEU
Chi-restraints excluded: chain A residue 1266 LEU
Chi-restraints excluded: chain A residue 1351 LEU
Chi-restraints excluded: chain A residue 1380 THR
Chi-restraints excluded: chain A residue 1381 MET
Chi-restraints excluded: chain A residue 1405 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 96 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 103 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 45 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 111 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.4105 r_free = 0.4105 target = 0.195679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.163308 restraints weight = 10340.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 1.40
r_work: 0.3247 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2331

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9900  Z= 0.151
  Angle     :  0.517   8.541  13401  Z= 0.277
  Chirality :  0.040   0.159   1570
  Planarity :  0.004   0.060   1680
  Dihedral  :  4.437  68.572   1337
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 20.15 %
    Favored  : 76.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.24), residues: 1228
  helix:  1.83 (0.18), residues: 797
  sheet:  1.26 (0.74), residues: 51
  loop : -1.05 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A1097 
 HIS   0.002   0.001   HIS A1121 
 PHE   0.015   0.001   PHE A 434 
 TYR   0.012   0.001   TYR A1135 
 ARG   0.002   0.000   ARG A 703 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06665 (  645)
  hydrogen bonds       : angle       4.46528 ( 1896)
  covalent geometry    : bond        0.00320 ( 9900)
  covalent geometry    : angle       0.51699 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 121
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7974 (pttm)
REVERT: A  360 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7791 (mt-10)
REVERT: A  491 GLU cc_start: 0.7399 (tt0) cc_final: 0.6650 (pp20)
REVERT: A  493 LYS cc_start: 0.8573 (mptp) cc_final: 0.8344 (mptm)
REVERT: A  586 GLN cc_start: 0.7769 (mt0) cc_final: 0.6807 (tt0)
REVERT: A  589 LYS cc_start: 0.7680 (mtpt) cc_final: 0.7143 (mmtm)
REVERT: A  631 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7751 (mt0)
REVERT: A  953 ARG cc_start: 0.8083 (ttm-80) cc_final: 0.7750 (ttp80)
REVERT: A  980 ASP cc_start: 0.8746 (t70) cc_final: 0.8496 (t0)
REVERT: A 1040 LYS cc_start: 0.8165 (tttm) cc_final: 0.7806 (tttp)
REVERT: A 1095 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7826 (mpp)
REVERT: A 1166 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.6358 (t80)
REVERT: A 1221 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7414 (mt-10)
REVERT: A 1238 MET cc_start: 0.8127 (tpp) cc_final: 0.7875 (ttm)
REVERT: A 1381 MET cc_start: 0.6142 (OUTLIER) cc_final: 0.4456 (tmm)
  outliers start: 38
  outliers final: 18
  residues processed: 148
  average time/residue: 1.0809
  time to fit residues: 173.1266
Evaluate side-chains
  137 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LYS
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  704 SER
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  877 THR
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1048 SER
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1154 GLU
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1272 ILE
Chi-restraints excluded: chain A residue 1351 LEU
Chi-restraints excluded: chain A residue 1380 THR
Chi-restraints excluded: chain A residue 1381 MET
Chi-restraints excluded: chain A residue 1405 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 94 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 103 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.186774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.123342 restraints weight = 10466.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3377 rms_B_bonded: 1.60
r_work: 0.3260 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3144 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9900  Z= 0.162
  Angle     :  0.547  10.995  13401  Z= 0.292
  Chirality :  0.041   0.248   1570
  Planarity :  0.004   0.060   1680
  Dihedral  :  4.434  67.625   1337
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.28 %
    Favored  : 75.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.24), residues: 1228
  helix:  1.85 (0.18), residues: 790
  sheet:  1.20 (0.74), residues: 51
  loop : -0.92 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A1121 
 PHE   0.020   0.001   PHE A 434 
 TYR   0.012   0.001   TYR A1135 
 ARG   0.002   0.000   ARG A 703 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06900 (  645)
  hydrogen bonds       : angle       4.48847 ( 1896)
  covalent geometry    : bond        0.00348 ( 9900)
  covalent geometry    : angle       0.54706 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 120
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8006 (pttm)
REVERT: A  360 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7857 (mt-10)
REVERT: A  491 GLU cc_start: 0.7493 (tt0) cc_final: 0.6782 (pp20)
REVERT: A  586 GLN cc_start: 0.7824 (mt0) cc_final: 0.6796 (tt0)
REVERT: A  589 LYS cc_start: 0.7740 (mtpt) cc_final: 0.7318 (mttm)
REVERT: A  631 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7754 (mp10)
REVERT: A  953 ARG cc_start: 0.8161 (ttm-80) cc_final: 0.7871 (ttp80)
REVERT: A  980 ASP cc_start: 0.8756 (t70) cc_final: 0.8511 (t0)
REVERT: A 1040 LYS cc_start: 0.8299 (tttm) cc_final: 0.8048 (tttp)
REVERT: A 1095 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7895 (mpp)
REVERT: A 1166 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.6422 (t80)
REVERT: A 1221 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7544 (mt-10)
REVERT: A 1238 MET cc_start: 0.8247 (tpp) cc_final: 0.8016 (ttm)
  outliers start: 30
  outliers final: 17
  residues processed: 143
  average time/residue: 1.0378
  time to fit residues: 161.0264
Evaluate side-chains
  136 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LYS
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  279 ILE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain A residue  841 VAL
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1048 SER
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1154 GLU
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1351 LEU
Chi-restraints excluded: chain A residue 1380 THR
Chi-restraints excluded: chain A residue 1405 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** 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 = 0.3993 r_free = 0.3993 target = 0.186246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.122664 restraints weight = 10408.866|
|-----------------------------------------------------------------------------|
r_work (start): 0.3304 rms_B_bonded: 1.84
r_work: 0.3172 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9900  Z= 0.161
  Angle     :  0.543   9.412  13401  Z= 0.289
  Chirality :  0.041   0.166   1570
  Planarity :  0.004   0.060   1680
  Dihedral  :  4.456  67.519   1337
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.09 %
    Favored  : 75.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.24), residues: 1228
  helix:  1.86 (0.18), residues: 790
  sheet:  1.04 (0.75), residues: 51
  loop : -0.90 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1097 
 HIS   0.005   0.001   HIS A 487 
 PHE   0.017   0.001   PHE A 434 
 TYR   0.012   0.001   TYR A1135 
 ARG   0.002   0.000   ARG A 703 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06854 (  645)
  hydrogen bonds       : angle       4.48746 ( 1896)
  covalent geometry    : bond        0.00347 ( 9900)
  covalent geometry    : angle       0.54316 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 119
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  138 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8036 (pttm)
REVERT: A  360 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7758 (mt-10)
REVERT: A  448 LYS cc_start: 0.6772 (OUTLIER) cc_final: 0.6030 (ptpt)
REVERT: A  491 GLU cc_start: 0.7501 (tt0) cc_final: 0.6558 (pp20)
REVERT: A  493 LYS cc_start: 0.8558 (mptm) cc_final: 0.8314 (mptm)
REVERT: A  586 GLN cc_start: 0.8040 (mt0) cc_final: 0.7813 (mt0)
REVERT: A  589 LYS cc_start: 0.7776 (mtpt) cc_final: 0.7275 (mttm)
REVERT: A  631 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7694 (mp10)
REVERT: A  641 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7331 (m-30)
REVERT: A  953 ARG cc_start: 0.8062 (ttm-80) cc_final: 0.7670 (ttp80)
REVERT: A  980 ASP cc_start: 0.8743 (t70) cc_final: 0.8487 (t0)
REVERT: A 1095 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.7862 (mpp)
REVERT: A 1166 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.6283 (t80)
REVERT: A 1221 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7440 (mt-10)
REVERT: A 1238 MET cc_start: 0.8083 (tpp) cc_final: 0.7841 (ttm)
  outliers start: 33
  outliers final: 19
  residues processed: 143
  average time/residue: 1.0917
  time to fit residues: 169.8568
Evaluate side-chains
  140 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LYS
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  448 LYS
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  608 ILE
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  704 SER
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain A residue  841 VAL
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  877 THR
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1048 SER
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1095 MET
Chi-restraints excluded: chain A residue 1154 GLU
Chi-restraints excluded: chain A residue 1166 TYR
Chi-restraints excluded: chain A residue 1380 THR
Chi-restraints excluded: chain A residue 1405 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 122 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 108 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 67 optimal weight:    8.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** 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 = 0.3952 r_free = 0.3952 target = 0.181569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.117896 restraints weight = 10503.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.85
r_work: 0.3032 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.072   9900  Z= 0.251
  Angle     :  0.632   9.109  13401  Z= 0.337
  Chirality :  0.045   0.201   1570
  Planarity :  0.005   0.070   1680
  Dihedral  :  4.647  63.267   1337
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 21.85 %
    Favored  : 75.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.24), residues: 1228
  helix:  1.64 (0.18), residues: 784
  sheet:  0.71 (0.72), residues: 51
  loop : -0.89 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 633 
 HIS   0.006   0.001   HIS A1121 
 PHE   0.025   0.002   PHE A 434 
 TYR   0.012   0.002   TYR A1135 
 ARG   0.005   0.001   ARG A 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08470 (  645)
  hydrogen bonds       : angle       4.77753 ( 1896)
  covalent geometry    : bond        0.00592 ( 9900)
  covalent geometry    : angle       0.63192 (13401)

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

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

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2456 Ramachandran restraints generated.
    1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 115
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8034 (pttm)
REVERT: A  491 GLU cc_start: 0.7581 (tt0) cc_final: 0.6480 (pp20)
REVERT: A  493 LYS cc_start: 0.8478 (mptm) cc_final: 0.8258 (mptp)
REVERT: A  586 GLN cc_start: 0.7980 (mt0) cc_final: 0.7685 (mt0)
REVERT: A  589 LYS cc_start: 0.7707 (mtpt) cc_final: 0.7238 (mttm)
REVERT: A  630 GLN cc_start: 0.7476 (mt0) cc_final: 0.6710 (pm20)
REVERT: A  641 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7308 (m-30)
REVERT: A  710 ASP cc_start: 0.6922 (OUTLIER) cc_final: 0.6390 (p0)
REVERT: A 1040 LYS cc_start: 0.8055 (tttm) cc_final: 0.7663 (tttp)
REVERT: A 1116 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8124 (mmt)
REVERT: A 1221 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7301 (mt-10)
REVERT: A 1238 MET cc_start: 0.7820 (tpp) cc_final: 0.7487 (ttm)
REVERT: A 1265 ASP cc_start: 0.7535 (m-30) cc_final: 0.6896 (t0)
  outliers start: 27
  outliers final: 17
  residues processed: 137
  average time/residue: 1.1345
  time to fit residues: 168.5912
Evaluate side-chains
  133 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  138 LYS
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  303 VAL
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  631 GLN
Chi-restraints excluded: chain A residue  641 ASP
Chi-restraints excluded: chain A residue  704 SER
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  710 ASP
Chi-restraints excluded: chain A residue  841 VAL
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  877 THR
Chi-restraints excluded: chain A residue  901 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1048 SER
Chi-restraints excluded: chain A residue 1052 SER
Chi-restraints excluded: chain A residue 1116 MET
Chi-restraints excluded: chain A residue 1154 GLU
Chi-restraints excluded: chain A residue 1380 THR
Chi-restraints excluded: chain A residue 1405 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 101 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 112 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 114 optimal weight:    8.9990
   chunk 93 optimal weight:    0.7980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 631 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.185001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.136206 restraints weight = 10381.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 2.56
r_work: 0.3234 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9900  Z= 0.153
  Angle     :  0.548   9.100  13401  Z= 0.291
  Chirality :  0.041   0.172   1570
  Planarity :  0.004   0.060   1680
  Dihedral  :  4.518  67.255   1337
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 22.41 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.08 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.24), residues: 1228
  helix:  1.87 (0.18), residues: 784
  sheet:  0.93 (0.73), residues: 51
  loop : -0.85 (0.30), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1097 
 HIS   0.004   0.001   HIS A 421 
 PHE   0.021   0.001   PHE A1330 
 TYR   0.012   0.001   TYR A1135 
 ARG   0.003   0.000   ARG A1096 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06860 (  645)
  hydrogen bonds       : angle       4.54377 ( 1896)
  covalent geometry    : bond        0.00316 ( 9900)
  covalent geometry    : angle       0.54784 (13401)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 7345.14 seconds
wall clock time: 127 minutes 19.79 seconds (7639.79 seconds total)