Starting phenix.real_space_refine
on Tue Jul 29 05:56:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dmy_7968/07_2025/6dmy_7968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dmy_7968/07_2025/6dmy_7968.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dmy_7968/07_2025/6dmy_7968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dmy_7968/07_2025/6dmy_7968.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dmy_7968/07_2025/6dmy_7968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dmy_7968/07_2025/6dmy_7968.cif"
  }
  resolution = 3.6
  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=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1998 atoms to isotropic.
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      1      6.06       5
     S      47      5.16       5
     C    5978      2.51       5
     N    1510      2.21       5
     O    1673      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9211
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 992, 7821
          Classifications: {'peptide': 992}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 42, 'TRANS': 947}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 24
    Chain: "B"
      Number of atoms: 1213
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 1213
          Classifications: {'peptide': 151}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 145}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 140
          Unusual residues: {'NAG': 5, 'Y01': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
    Chain: "B"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Classifications: {'peptide': 1}
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 5.54, per 1000 atoms: 0.60
  Number of scatterers: 9211
  At special positions: 0
  Unit cell: (92.735, 86.189, 152.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Ca      2     19.99
     S      47     16.00
     O    1673      8.00
     N    1510      7.00
     C    5978      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 226 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 327 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 296 " - pdb=" SG  CYS A 304 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG A1801 " - " ASN A 312 "
      " NAG A1802 " - " ASN A 349 "
      " NAG A1803 " - " ASN A 414 "
      " NAG A1804 " - " ASN A 875 "
      " NAG A1807 " - " ASN A 141 "
      " NAG C   1 " - " ASN A1000 "
    TRANS
      " SER B 201 " - " ASN B 189 "
  Time building additional restraints: 2.15
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 202 "
        pdb="ZN    ZN B 202 " - pdb=" NE2 HIS B 140 "
        pdb="ZN    ZN B 202 " - pdb=" ND1 HIS B 182 "


  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2144

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      53.7% alpha, 4.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 96
      removed outlier: 3.727A  pdb=" N   TRP A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   LEU A  86 " --> pdb=" O   LYS A  82 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   LEU A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LYS A  89 " --> pdb=" O   ARG A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 115
      removed outlier: 3.811A  pdb=" N   LEU A 102 " --> pdb=" O   CYS A  98 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   ALA A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   PHE A 112 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA A 113 " --> pdb=" O   PHE A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 144
    Processing helix  chain 'A' and resid 171 through 185
    Processing helix  chain 'A' and resid 198 through 203
      removed outlier: 3.675A  pdb=" N   LEU A 202 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 223
      removed outlier: 3.566A  pdb=" N   GLN A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ILE A 219 " --> pdb=" O   TYR A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 234
      removed outlier: 3.764A  pdb=" N   ASP A 233 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 267
    Processing helix  chain 'A' and resid 275 through 285
      removed outlier: 3.564A  pdb=" N   GLU A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 343
    Processing helix  chain 'A' and resid 368 through 376
    Processing helix  chain 'A' and resid 388 through 410
      removed outlier: 3.656A  pdb=" N   SER A 410 " --> pdb=" O   VAL A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 435
    Processing helix  chain 'A' and resid 438 through 457
      removed outlier: 3.757A  pdb=" N   LEU A 455 " --> pdb=" O   ALA A 451 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   MET A 457 " --> pdb=" O   ALA A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 489
      removed outlier: 3.525A  pdb=" N   LEU A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 525
      Proline residue:  A 504  - end of helix
      removed outlier: 3.636A  pdb=" N   GLY A 509 " --> pdb=" O   PHE A 505 " (cutoff:3.500A)
      removed outlier: 4.766A  pdb=" N   ASP A 513 " --> pdb=" O   GLY A 509 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   ASP A 514 " --> pdb=" O   VAL A 510 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   VAL A 515 " --> pdb=" O   GLY A 511 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   THR A 525 " --> pdb=" O   ALA A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 543
    Processing helix  chain 'A' and resid 544 through 564
      removed outlier: 3.611A  pdb=" N   SER A 552 " --> pdb=" O   VAL A 548 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA A 558 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 605
      removed outlier: 3.984A  pdb=" N   GLN A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      Proline residue:  A 593  - end of helix
      removed outlier: 4.723A  pdb=" N   ASP A 605 " --> pdb=" O   TYR A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 735
    Processing helix  chain 'A' and resid 740 through 745
    Processing helix  chain 'A' and resid 750 through 769
      removed outlier: 3.828A  pdb=" N   ILE A 754 " --> pdb=" O   LYS A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 795
    Processing helix  chain 'A' and resid 816 through 826
      removed outlier: 3.568A  pdb=" N   TYR A 820 " --> pdb=" O   GLN A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 830
      removed outlier: 3.847A  pdb=" N   LYS A 830 " --> pdb=" O   SER A 827 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 827 through 830'
    Processing helix  chain 'A' and resid 843 through 863
    Processing helix  chain 'A' and resid 881 through 889
      removed outlier: 3.790A  pdb=" N   VAL A 888 " --> pdb=" O   TYR A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 904
      removed outlier: 3.695A  pdb=" N   GLN A 901 " --> pdb=" O   ASP A 898 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   LYS A 904 " --> pdb=" O   GLN A 901 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 920 through 930
    Processing helix  chain 'A' and resid 930 through 937
    Processing helix  chain 'A' and resid 983 through 1002
      removed outlier: 3.825A  pdb=" N   PHE A 987 " --> pdb=" O   ASP A 983 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1018
    Processing helix  chain 'A' and resid 1026 through 1046
      removed outlier: 3.771A  pdb=" N   PHE A1040 " --> pdb=" O   LEU A1036 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1075
      removed outlier: 3.910A  pdb=" N   ILE A1055 " --> pdb=" O   TRP A1051 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE A1056 " --> pdb=" O   THR A1052 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1107
      removed outlier: 3.558A  pdb=" N   ILE A1085 " --> pdb=" O   VAL A1081 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   GLU A1095 " --> pdb=" O   GLY A1091 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   PHE A1096 " --> pdb=" O   ILE A1092 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   THR A1097 " --> pdb=" O   GLY A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1122
      removed outlier: 3.541A  pdb=" N   LEU A1117 " --> pdb=" O   ARG A1113 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   MET A1122 " --> pdb=" O   ALA A1118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1141
      removed outlier: 4.747A  pdb=" N   THR A1133 " --> pdb=" O   GLY A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1152
      removed outlier: 3.934A  pdb=" N   VAL A1149 " --> pdb=" O   PHE A1145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1178
      removed outlier: 4.306A  pdb=" N   ILE A1158 " --> pdb=" O   ALA A1154 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   ILE A1161 " --> pdb=" O   ALA A1157 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU A1162 " --> pdb=" O   ILE A1158 " (cutoff:3.500A)
      Proline residue:  A1172  - end of helix
      removed outlier: 3.596A  pdb=" N   PHE A1177 " --> pdb=" O   VAL A1173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 74
      removed outlier: 3.586A  pdb=" N   PHE B  73 " --> pdb=" O   SER B  70 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   LYS B  74 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 70 through 74'
    Processing helix  chain 'B' and resid 99 through 115
    Processing helix  chain 'B' and resid 138 through 142
    Processing helix  chain 'B' and resid 157 through 167
    Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229
      removed outlier: 3.612A  pdb=" N   LEU A 360 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   LEU A 157 " --> pdb=" O   PHE A 422 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE A 422 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 328
    Processing sheet with id=AA3, first strand: chain 'A' and resid 972 through 978
      removed outlier: 3.593A  pdb=" N   ALA A 972 " --> pdb=" O   THR A 807 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   TYR A 804 " --> pdb=" O   ASN A1011 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   SER A1007 " --> pdb=" O   GLN A 808 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 48
      removed outlier: 3.693A  pdb=" N   ILE B  48 " --> pdb=" O   VAL B 173 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   VAL B 173 " --> pdb=" O   ILE B  48 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ASP B 147 " --> pdb=" O   THR B 125 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   ILE B  85 " --> pdb=" O   VAL B 124 " (cutoff:3.500A)
      removed outlier: 7.501A  pdb=" N   GLU B 126 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)

    423 hydrogen bonds defined for protein.
    1236 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.60

  Time building geometry restraints manager: 2.58 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2653
        1.34 -     1.46: 2402
        1.46 -     1.59: 4300
        1.59 -     1.71: 0
        1.71 -     1.84: 77
  Bond restraints: 9432
  Sorted by residual:
  bond pdb=" CAY Y01 A1809 "
       pdb=" OAW Y01 A1809 "
    ideal  model  delta    sigma   weight residual
    1.332  1.457 -0.125 2.00e-02 2.50e+03 3.91e+01
  bond pdb=" CAY Y01 A1808 "
       pdb=" OAW Y01 A1808 "
    ideal  model  delta    sigma   weight residual
    1.332  1.445 -0.113 2.00e-02 2.50e+03 3.20e+01
  bond pdb=" C   ASN A 915 "
       pdb=" N   PRO A 916 "
    ideal  model  delta    sigma   weight residual
    1.334  1.220  0.114 2.34e-02 1.83e+03 2.36e+01
  bond pdb=" CA  ASN A1011 "
       pdb=" C   ASN A1011 "
    ideal  model  delta    sigma   weight residual
    1.521  1.575 -0.054 1.20e-02 6.94e+03 2.01e+01
  bond pdb=" CAX Y01 A1809 "
       pdb=" OAH Y01 A1809 "
    ideal  model  delta    sigma   weight residual
    1.248  1.329 -0.081 2.00e-02 2.50e+03 1.65e+01
  ... (remaining 9427 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.63: 12597
        4.63 -     9.26: 201
        9.26 -    13.89: 21
       13.89 -    18.52: 4
       18.52 -    23.15: 2
  Bond angle restraints: 12825
  Sorted by residual:
  angle pdb=" C   TYR A1181 "
        pdb=" N   PRO A1182 "
        pdb=" CA  PRO A1182 "
      ideal   model   delta    sigma   weight residual
     119.84  142.99  -23.15 1.25e+00 6.40e-01 3.43e+02
  angle pdb=" C   GLY A1179 "
        pdb=" N   PRO A1180 "
        pdb=" CA  PRO A1180 "
      ideal   model   delta    sigma   weight residual
     119.05  133.69  -14.64 1.11e+00 8.12e-01 1.74e+02
  angle pdb=" N   TYR A 873 "
        pdb=" CA  TYR A 873 "
        pdb=" C   TYR A 873 "
      ideal   model   delta    sigma   weight residual
     111.36  123.86  -12.50 1.09e+00 8.42e-01 1.32e+02
  angle pdb=" CA  PRO A 896 "
        pdb=" N   PRO A 896 "
        pdb=" CD  PRO A 896 "
      ideal   model   delta    sigma   weight residual
     112.00   99.49   12.51 1.40e+00 5.10e-01 7.98e+01
  angle pdb=" N   LEU A 777 "
        pdb=" CA  LEU A 777 "
        pdb=" C   LEU A 777 "
      ideal   model   delta    sigma   weight residual
     111.28  119.15   -7.87 1.09e+00 8.42e-01 5.22e+01
  ... (remaining 12820 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.65: 5472
       24.65 -    49.29: 244
       49.29 -    73.94: 43
       73.94 -    98.59: 16
       98.59 -   123.23: 3
  Dihedral angle restraints: 5778
    sinusoidal: 2443
      harmonic: 3335
  Sorted by residual:
  dihedral pdb=" CB  CYS A 296 "
           pdb=" SG  CYS A 296 "
           pdb=" SG  CYS A 304 "
           pdb=" CB  CYS A 304 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -179.64  -87.36     1      1.00e+01 1.00e-02 9.16e+01
  dihedral pdb=" CA  PRO A 316 "
           pdb=" C   PRO A 316 "
           pdb=" N   LEU A 317 "
           pdb=" CA  LEU A 317 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.22   40.78     0      5.00e+00 4.00e-02 6.65e+01
  dihedral pdb=" CA  TYR A 224 "
           pdb=" C   TYR A 224 "
           pdb=" N   PRO A 225 "
           pdb=" CA  PRO A 225 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -139.31  -40.69     0      5.00e+00 4.00e-02 6.62e+01
  ... (remaining 5775 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1301
       0.104 -    0.207: 150
       0.207 -    0.310: 15
       0.310 -    0.414: 2
       0.414 -    0.517: 3
  Chirality restraints: 1471
  Sorted by residual:
  chirality pdb=" CG  LEU A 476 "
            pdb=" CB  LEU A 476 "
            pdb=" CD1 LEU A 476 "
            pdb=" CD2 LEU A 476 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.07   -0.52 2.00e-01 2.50e+01 6.69e+00
  chirality pdb=" CA  TYR A 873 "
            pdb=" N   TYR A 873 "
            pdb=" C   TYR A 873 "
            pdb=" CB  TYR A 873 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.04e+00
  chirality pdb=" CB  ILE A 531 "
            pdb=" CA  ILE A 531 "
            pdb=" CG1 ILE A 531 "
            pdb=" CG2 ILE A 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.23    0.42 2.00e-01 2.50e+01 4.39e+00
  ... (remaining 1468 not shown)

  Planarity restraints: 1608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 895 "   -0.096 5.00e-02 4.00e+02   1.35e-01 2.90e+01
        pdb=" N   PRO A 896 "    0.232 5.00e-02 4.00e+02
        pdb=" CA  PRO A 896 "   -0.068 5.00e-02 4.00e+02
        pdb=" CD  PRO A 896 "   -0.067 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 774 "    0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   GLY A 774 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   GLY A 774 "    0.022 2.00e-02 2.50e+03
        pdb=" N   LEU A 775 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 317 "    0.016 2.00e-02 2.50e+03   3.20e-02 1.02e+01
        pdb=" C   LEU A 317 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   LEU A 317 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASP A 318 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1605 not shown)

  Histogram of nonbonded interaction distances:
        1.72 -     2.35: 34
        2.35 -     2.99: 4483
        2.99 -     3.63: 13813
        3.63 -     4.26: 20110
        4.26 -     4.90: 33236
  Nonbonded interactions: 71676
  Sorted by model distance:
  nonbonded pdb=" CB  ARG A 906 "
            pdb=" OD2 ASP A 909 "
     model   vdw
     1.716 3.440
  nonbonded pdb=" O   GLU A 122 "
            pdb=" ND2 ASN A 124 "
     model   vdw
     1.799 3.120
  nonbonded pdb=" O   GLY A 866 "
            pdb=" CD1 ILE A 868 "
     model   vdw
     2.006 3.460
  nonbonded pdb=" O   LEU A 317 "
            pdb=" OD1 ASP A 318 "
     model   vdw
     2.046 3.040
  nonbonded pdb=" OD2 ASP B 147 "
            pdb="ZN    ZN B 202 "
     model   vdw
     2.084 2.230
  ... (remaining 71671 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.520
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
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      :  0.011   0.645   9445  Z= 0.467
  Angle     :  1.451  23.146  12855  Z= 0.771
  Chirality :  0.074   0.517   1471
  Planarity :  0.009   0.135   1601
  Dihedral  : 15.160 123.235   3622
  Min Nonbonded Distance : 1.716

Molprobity Statistics.
  All-atom Clashscore : 15.96
  Ramachandran Plot:
    Outliers :  1.06 %
    Allowed  : 11.61 %
    Favored  : 87.34 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  :  8.61 %
    Favored  : 87.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 4.17 %
    Twisted General : 0.73 %

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: -4.80 (0.19), residues: 1137
  helix: -3.04 (0.14), residues: 607
  sheet: -2.67 (0.61), residues: 65
  loop : -3.30 (0.25), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.004   TRP A 399 
 HIS   0.015   0.004   HIS A 739 
 PHE   0.033   0.004   PHE A 422 
 TYR   0.026   0.004   TYR A 224 
 ARG   0.009   0.001   ARG B 163 

Details of bonding type rmsd
  link_TRANS           : bond        0.00227 (    1)
  link_TRANS           : angle       0.75485 (    3)
  link_NAG-ASN         : bond        0.00601 (    6)
  link_NAG-ASN         : angle       4.32800 (   18)
  link_BETA1-4         : bond        0.01219 (    1)
  link_BETA1-4         : angle       5.63780 (    3)
  hydrogen bonds       : bond        0.16075 (  423)
  hydrogen bonds       : angle      10.28640 ( 1236)
  metal coordination   : bond        0.46410 (    2)
  SS BOND              : bond        0.00309 (    3)
  SS BOND              : angle       2.33325 (    6)
  covalent geometry    : bond        0.00912 ( 9432)
  covalent geometry    : angle       1.44008 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 319
  time to evaluate  : 1.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6708 (mp)
REVERT: A  422 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8397 (p90)
REVERT: A  487 LEU cc_start: 0.8397 (tm) cc_final: 0.8160 (tp)
REVERT: A  740 TYR cc_start: 0.7498 (t80) cc_final: 0.7063 (t80)
REVERT: A  777 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6511 (mt)
REVERT: A  956 MET cc_start: 0.7044 (ppp) cc_final: 0.6719 (ppp)
REVERT: A  960 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6641 (ttt180)
REVERT: A 1013 TYR cc_start: 0.7886 (m-10) cc_final: 0.7653 (m-10)
REVERT: A 1046 PHE cc_start: 0.7700 (m-10) cc_final: 0.7498 (m-80)
REVERT: A 1051 TRP cc_start: 0.6439 (t-100) cc_final: 0.5356 (m-10)
REVERT: A 1055 ILE cc_start: 0.7874 (mm) cc_final: 0.7660 (mt)
  outliers start: 36
  outliers final: 16
  residues processed: 340
  average time/residue: 0.2674
  time to fit residues: 119.7390
Evaluate side-chains
  184 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ASN
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  138 ARG
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  868 ILE
Chi-restraints excluded: chain A residue  873 TYR
Chi-restraints excluded: chain A residue  874 LYS
Chi-restraints excluded: chain A residue  882 LEU
Chi-restraints excluded: chain A residue  960 ARG
Chi-restraints excluded: chain A residue 1077 LYS
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain B residue  129 ASP
Chi-restraints excluded: chain B residue  188 GLU
Chi-restraints excluded: chain B residue  201 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    8.9990
   chunk 89 optimal weight:    0.9980
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:   30.0000
   chunk 66 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 156 GLN
A 160 GLN
A 274 GLN
A 324 ASN
A 328 HIS
A 336 HIS
A 384 HIS
A 802 ASN
A 929 ASN
** A 940 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1121 HIS
B  81 ASN
B 180 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.144556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.129155 restraints weight = 18596.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.131743 restraints weight = 10493.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.133381 restraints weight = 7157.366|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   9445  Z= 0.175
  Angle     :  0.916  19.805  12855  Z= 0.450
  Chirality :  0.050   0.349   1471
  Planarity :  0.006   0.058   1601
  Dihedral  : 11.989 101.773   1575
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  9.85 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 15.04 %
    Favored  : 79.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.08 %
    Twisted General : 0.27 %

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: -2.99 (0.23), residues: 1137
  helix: -1.26 (0.19), residues: 627
  sheet: -1.99 (0.59), residues: 68
  loop : -2.99 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 844 
 HIS   0.006   0.001   HIS A 289 
 PHE   0.017   0.002   PHE A 795 
 TYR   0.038   0.002   TYR A1181 
 ARG   0.005   0.001   ARG A 942 

Details of bonding type rmsd
  link_TRANS           : bond        0.00016 (    1)
  link_TRANS           : angle       0.45720 (    3)
  link_NAG-ASN         : bond        0.00307 (    6)
  link_NAG-ASN         : angle       4.28863 (   18)
  link_BETA1-4         : bond        0.00445 (    1)
  link_BETA1-4         : angle       3.12860 (    3)
  hydrogen bonds       : bond        0.05349 (  423)
  hydrogen bonds       : angle       5.69604 ( 1236)
  metal coordination   : bond        0.00665 (    2)
  SS BOND              : bond        0.00103 (    3)
  SS BOND              : angle       1.34704 (    6)
  covalent geometry    : bond        0.00378 ( 9432)
  covalent geometry    : angle       0.90076 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 188
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6402 (pt)
REVERT: A  101 PHE cc_start: 0.3821 (OUTLIER) cc_final: 0.2603 (t80)
REVERT: A  128 LEU cc_start: 0.7613 (OUTLIER) cc_final: 0.7338 (mp)
REVERT: A  135 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7560 (ttp-110)
REVERT: A  422 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7423 (p90)
REVERT: A  487 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8264 (tp)
REVERT: A  584 ASN cc_start: 0.8592 (t0) cc_final: 0.8382 (t0)
REVERT: A  740 TYR cc_start: 0.7322 (t80) cc_final: 0.6894 (t80)
REVERT: A  777 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6772 (mt)
REVERT: A  804 TYR cc_start: 0.8250 (m-80) cc_final: 0.8000 (m-80)
REVERT: A 1051 TRP cc_start: 0.6514 (t-100) cc_final: 0.5654 (m-10)
REVERT: A 1055 ILE cc_start: 0.8165 (mm) cc_final: 0.7837 (mt)
REVERT: A 1070 MET cc_start: 0.8030 (tpp) cc_final: 0.7781 (tpp)
REVERT: A 1183 GLU cc_start: 0.6089 (pt0) cc_final: 0.5789 (pt0)
  outliers start: 54
  outliers final: 19
  residues processed: 226
  average time/residue: 0.2233
  time to fit residues: 70.0375
Evaluate side-chains
  174 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  135 ARG
Chi-restraints excluded: chain A residue  138 ARG
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  409 GLN
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  475 LEU
Chi-restraints excluded: chain A residue  487 LEU
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  873 TYR
Chi-restraints excluded: chain A residue  874 LYS
Chi-restraints excluded: chain A residue  882 LEU
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1077 LYS
Chi-restraints excluded: chain A residue 1078 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 42 optimal weight:    0.0770
   chunk 24 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   chunk 55 optimal weight:    0.5980
   chunk 83 optimal weight:    0.3980
   chunk 21 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 43 optimal weight:    7.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A 328 HIS
** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 940 ASN
A 944 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.142839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.127316 restraints weight = 18809.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.129967 restraints weight = 10517.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.131659 restraints weight = 7105.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.4277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9445  Z= 0.149
  Angle     :  0.809  13.855  12855  Z= 0.397
  Chirality :  0.047   0.263   1471
  Planarity :  0.005   0.056   1601
  Dihedral  :  9.360  58.101   1558
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.76 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 17.84 %
    Favored  : 77.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.08 %
    Twisted General : 0.09 %

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: -2.08 (0.24), residues: 1137
  helix: -0.41 (0.20), residues: 629
  sheet: -1.23 (0.60), residues: 70
  loop : -2.85 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 844 
 HIS   0.004   0.001   HIS A 846 
 PHE   0.019   0.001   PHE A 235 
 TYR   0.032   0.002   TYR A 224 
 ARG   0.005   0.001   ARG A 536 

Details of bonding type rmsd
  link_TRANS           : bond        0.00069 (    1)
  link_TRANS           : angle       0.31463 (    3)
  link_NAG-ASN         : bond        0.00513 (    6)
  link_NAG-ASN         : angle       3.15676 (   18)
  link_BETA1-4         : bond        0.00194 (    1)
  link_BETA1-4         : angle       2.71171 (    3)
  hydrogen bonds       : bond        0.04500 (  423)
  hydrogen bonds       : angle       4.88856 ( 1236)
  metal coordination   : bond        0.00243 (    2)
  SS BOND              : bond        0.00146 (    3)
  SS BOND              : angle       1.26378 (    6)
  covalent geometry    : bond        0.00313 ( 9432)
  covalent geometry    : angle       0.79967 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 167
  time to evaluate  : 0.988 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  101 PHE cc_start: 0.4208 (OUTLIER) cc_final: 0.2993 (t80)
REVERT: A  128 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7012 (mt)
REVERT: A  135 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7523 (ttp-110)
REVERT: A  152 MET cc_start: 0.6079 (tpt) cc_final: 0.5772 (tpp)
REVERT: A  422 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7419 (p90)
REVERT: A  777 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6984 (mt)
REVERT: A  804 TYR cc_start: 0.8346 (m-80) cc_final: 0.8094 (m-80)
REVERT: A  981 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6246 (pp)
REVERT: A 1051 TRP cc_start: 0.6364 (t-100) cc_final: 0.5486 (m-10)
REVERT: A 1055 ILE cc_start: 0.8178 (mm) cc_final: 0.7914 (mt)
REVERT: A 1070 MET cc_start: 0.8111 (tpp) cc_final: 0.7880 (tpp)
REVERT: B  177 SER cc_start: 0.8900 (t) cc_final: 0.8599 (t)
  outliers start: 47
  outliers final: 26
  residues processed: 206
  average time/residue: 0.2212
  time to fit residues: 63.3036
Evaluate side-chains
  172 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 140
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  128 LEU
Chi-restraints excluded: chain A residue  135 ARG
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  289 HIS
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  874 LYS
Chi-restraints excluded: chain A residue  882 LEU
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue  947 GLU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1074 ILE
Chi-restraints excluded: chain A residue 1077 LYS
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain B residue   98 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 105 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 88 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 67 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 14 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 242 GLN
A 940 ASN
A 950 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.140876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.124888 restraints weight = 18866.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.127525 restraints weight = 10643.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.129195 restraints weight = 7218.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.4848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9445  Z= 0.137
  Angle     :  0.752  13.209  12855  Z= 0.369
  Chirality :  0.045   0.252   1471
  Planarity :  0.005   0.064   1601
  Dihedral  :  8.482  59.528   1551
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 9.82
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.94 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 19.71 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.08 %
    Twisted General : 0.09 %

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: -1.55 (0.25), residues: 1137
  helix:  0.09 (0.21), residues: 635
  sheet: -0.95 (0.59), residues: 67
  loop : -2.77 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 844 
 HIS   0.005   0.001   HIS A 846 
 PHE   0.017   0.002   PHE A 848 
 TYR   0.033   0.001   TYR A 224 
 ARG   0.005   0.000   ARG A1114 

Details of bonding type rmsd
  link_TRANS           : bond        0.00033 (    1)
  link_TRANS           : angle       0.36733 (    3)
  link_NAG-ASN         : bond        0.00479 (    6)
  link_NAG-ASN         : angle       3.00046 (   18)
  link_BETA1-4         : bond        0.00068 (    1)
  link_BETA1-4         : angle       2.65793 (    3)
  hydrogen bonds       : bond        0.04112 (  423)
  hydrogen bonds       : angle       4.50833 ( 1236)
  metal coordination   : bond        0.00284 (    2)
  SS BOND              : bond        0.00111 (    3)
  SS BOND              : angle       1.15776 (    6)
  covalent geometry    : bond        0.00289 ( 9432)
  covalent geometry    : angle       0.74320 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 147
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6448 (pt)
REVERT: A  422 PHE cc_start: 0.7837 (OUTLIER) cc_final: 0.7381 (p90)
REVERT: A  740 TYR cc_start: 0.7585 (t80) cc_final: 0.7362 (t80)
REVERT: A  804 TYR cc_start: 0.8426 (m-80) cc_final: 0.8185 (m-80)
REVERT: A  981 LEU cc_start: 0.6937 (OUTLIER) cc_final: 0.6626 (pp)
REVERT: A 1051 TRP cc_start: 0.6393 (t-100) cc_final: 0.5462 (m-10)
REVERT: A 1055 ILE cc_start: 0.8171 (mm) cc_final: 0.7958 (mt)
REVERT: B  177 SER cc_start: 0.8881 (t) cc_final: 0.8527 (t)
  outliers start: 51
  outliers final: 30
  residues processed: 187
  average time/residue: 0.1980
  time to fit residues: 53.6355
Evaluate side-chains
  168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 135
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  289 HIS
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  865 THR
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  874 LYS
Chi-restraints excluded: chain A residue  882 LEU
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue  947 GLU
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1077 LYS
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain A residue 1183 GLU
Chi-restraints excluded: chain B residue  149 THR
Chi-restraints excluded: chain B residue  166 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 6 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 18 optimal weight:    0.3980
   chunk 46 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN
A 940 ASN
** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.123863 restraints weight = 18988.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.126426 restraints weight = 10666.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.128087 restraints weight = 7330.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7488
moved from start:          0.5210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9445  Z= 0.134
  Angle     :  0.752  12.289  12855  Z= 0.364
  Chirality :  0.045   0.248   1471
  Planarity :  0.005   0.056   1601
  Dihedral  :  8.031  59.561   1547
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.11 %
    Favored  : 89.71 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 21.06 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.17 (0.25), residues: 1137
  helix:  0.41 (0.21), residues: 635
  sheet: -0.84 (0.59), residues: 67
  loop : -2.61 (0.29), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 844 
 HIS   0.004   0.001   HIS A 846 
 PHE   0.016   0.001   PHE A 848 
 TYR   0.033   0.001   TYR A1181 
 ARG   0.005   0.000   ARG A1114 

Details of bonding type rmsd
  link_TRANS           : bond        0.00284 (    1)
  link_TRANS           : angle       0.19119 (    3)
  link_NAG-ASN         : bond        0.00435 (    6)
  link_NAG-ASN         : angle       3.03972 (   18)
  link_BETA1-4         : bond        0.00170 (    1)
  link_BETA1-4         : angle       2.67521 (    3)
  hydrogen bonds       : bond        0.03948 (  423)
  hydrogen bonds       : angle       4.33286 ( 1236)
  metal coordination   : bond        0.00271 (    2)
  SS BOND              : bond        0.00158 (    3)
  SS BOND              : angle       1.09941 (    6)
  covalent geometry    : bond        0.00288 ( 9432)
  covalent geometry    : angle       0.74285 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 148
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8726 (m)
REVERT: A  319 MET cc_start: 0.6297 (mmm) cc_final: 0.6076 (mmm)
REVERT: A  422 PHE cc_start: 0.7726 (OUTLIER) cc_final: 0.7373 (p90)
REVERT: A  496 ASN cc_start: 0.7447 (m-40) cc_final: 0.7197 (m110)
REVERT: A  981 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6830 (pp)
REVERT: A 1051 TRP cc_start: 0.6371 (t-100) cc_final: 0.5466 (m-10)
REVERT: A 1055 ILE cc_start: 0.8134 (mm) cc_final: 0.7888 (mt)
REVERT: A 1078 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8462 (mm)
REVERT: B  177 SER cc_start: 0.8877 (t) cc_final: 0.8463 (t)
REVERT: B  189 ASN cc_start: 0.6976 (m-40) cc_final: 0.6712 (m110)
  outliers start: 47
  outliers final: 31
  residues processed: 184
  average time/residue: 0.1879
  time to fit residues: 50.7277
Evaluate side-chains
  169 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 134
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  259 PHE
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  289 HIS
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  874 LYS
Chi-restraints excluded: chain A residue  882 LEU
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1077 LYS
Chi-restraints excluded: chain A residue 1078 LEU
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain A residue 1183 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 107 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 82 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0470
   chunk 34 optimal weight:    5.9990
   chunk 92 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN
A 940 ASN
** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.140345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.125043 restraints weight = 18683.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.127542 restraints weight = 10611.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.129134 restraints weight = 7328.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.5407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9445  Z= 0.128
  Angle     :  0.741  11.908  12855  Z= 0.357
  Chirality :  0.045   0.245   1471
  Planarity :  0.005   0.054   1601
  Dihedral  :  7.834  59.719   1546
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.64 %
    Favored  : 89.18 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 21.06 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.08 %
    Twisted General : 0.09 %

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: -0.97 (0.25), residues: 1137
  helix:  0.57 (0.21), residues: 632
  sheet: -0.73 (0.60), residues: 67
  loop : -2.51 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 844 
 HIS   0.004   0.001   HIS A 846 
 PHE   0.015   0.001   PHE A 848 
 TYR   0.031   0.001   TYR A 224 
 ARG   0.005   0.000   ARG A1114 

Details of bonding type rmsd
  link_TRANS           : bond        0.00001 (    1)
  link_TRANS           : angle       0.32975 (    3)
  link_NAG-ASN         : bond        0.00427 (    6)
  link_NAG-ASN         : angle       2.99020 (   18)
  link_BETA1-4         : bond        0.00004 (    1)
  link_BETA1-4         : angle       2.59484 (    3)
  hydrogen bonds       : bond        0.03840 (  423)
  hydrogen bonds       : angle       4.23814 ( 1236)
  metal coordination   : bond        0.00204 (    2)
  SS BOND              : bond        0.00148 (    3)
  SS BOND              : angle       1.05829 (    6)
  covalent geometry    : bond        0.00271 ( 9432)
  covalent geometry    : angle       0.73234 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 144
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6486 (pt)
REVERT: A  422 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.7394 (p90)
REVERT: A  501 GLN cc_start: 0.8071 (mp10) cc_final: 0.7769 (mp10)
REVERT: A  750 LYS cc_start: 0.6527 (mmpt) cc_final: 0.6059 (pttt)
REVERT: A  981 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6945 (pp)
REVERT: A 1051 TRP cc_start: 0.6412 (t-100) cc_final: 0.5508 (m-10)
REVERT: A 1055 ILE cc_start: 0.8139 (mm) cc_final: 0.7902 (mt)
REVERT: A 1077 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7782 (mmmm)
REVERT: B  177 SER cc_start: 0.8819 (t) cc_final: 0.8375 (t)
  outliers start: 49
  outliers final: 35
  residues processed: 181
  average time/residue: 0.1973
  time to fit residues: 53.4900
Evaluate side-chains
  171 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 132
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  259 PHE
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  289 HIS
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  771 VAL
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  882 LEU
Chi-restraints excluded: chain A residue  900 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1077 LYS
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain A residue 1183 GLU
Chi-restraints excluded: chain B residue  166 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 74 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 45 optimal weight:    0.2980
   chunk 3 optimal weight:   10.0000
   chunk 39 optimal weight:    0.7980
   chunk 104 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
A 361 GLN
A 371 GLN
A1099 HIS
** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.138221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.122794 restraints weight = 19036.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.125314 restraints weight = 10843.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.126940 restraints weight = 7437.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.5600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9445  Z= 0.140
  Angle     :  0.748  11.438  12855  Z= 0.364
  Chirality :  0.045   0.246   1471
  Planarity :  0.005   0.055   1601
  Dihedral  :  7.537  57.851   1540
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.47 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 22.41 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.08 %
    Twisted General : 0.09 %

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: -0.87 (0.26), residues: 1137
  helix:  0.67 (0.21), residues: 634
  sheet: -0.78 (0.60), residues: 67
  loop : -2.49 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 844 
 HIS   0.004   0.001   HIS A1099 
 PHE   0.018   0.001   PHE A 848 
 TYR   0.032   0.001   TYR A 224 
 ARG   0.005   0.000   ARG A1114 

Details of bonding type rmsd
  link_TRANS           : bond        0.00055 (    1)
  link_TRANS           : angle       0.31718 (    3)
  link_NAG-ASN         : bond        0.00414 (    6)
  link_NAG-ASN         : angle       3.05911 (   18)
  link_BETA1-4         : bond        0.00150 (    1)
  link_BETA1-4         : angle       2.74872 (    3)
  hydrogen bonds       : bond        0.03900 (  423)
  hydrogen bonds       : angle       4.20886 ( 1236)
  metal coordination   : bond        0.00317 (    2)
  SS BOND              : bond        0.00160 (    3)
  SS BOND              : angle       1.11338 (    6)
  covalent geometry    : bond        0.00307 ( 9432)
  covalent geometry    : angle       0.73818 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 137
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6465 (pt)
REVERT: A  361 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8537 (tt0)
REVERT: A  422 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7416 (p90)
REVERT: A  501 GLN cc_start: 0.8104 (mp10) cc_final: 0.7870 (mp10)
REVERT: A  750 LYS cc_start: 0.6572 (mmpt) cc_final: 0.6123 (pttt)
REVERT: A  756 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7598 (mt)
REVERT: A  981 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7136 (pp)
REVERT: A 1051 TRP cc_start: 0.6435 (t-100) cc_final: 0.5523 (m-10)
REVERT: A 1055 ILE cc_start: 0.8119 (mm) cc_final: 0.7893 (mt)
REVERT: B  177 SER cc_start: 0.8907 (t) cc_final: 0.8535 (t)
  outliers start: 48
  outliers final: 35
  residues processed: 174
  average time/residue: 0.1752
  time to fit residues: 44.8972
Evaluate side-chains
  169 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 129
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  259 PHE
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  289 HIS
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  328 HIS
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  882 LEU
Chi-restraints excluded: chain A residue  900 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1079 SER
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain A residue 1183 GLU
Chi-restraints excluded: chain B residue  166 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0570
   chunk 30 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 72 optimal weight:    0.4980
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN
A 371 GLN
A1099 HIS
** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.139521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.123767 restraints weight = 19206.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.126386 restraints weight = 10695.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.128009 restraints weight = 7247.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.5750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9445  Z= 0.127
  Angle     :  0.751  13.756  12855  Z= 0.361
  Chirality :  0.045   0.244   1471
  Planarity :  0.005   0.051   1601
  Dihedral  :  7.302  58.936   1536
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.38 %
    Favored  : 89.53 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 23.24 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.08 %
    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: -0.72 (0.26), residues: 1137
  helix:  0.81 (0.21), residues: 632
  sheet: -0.64 (0.60), residues: 67
  loop : -2.44 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 844 
 HIS   0.004   0.001   HIS A1099 
 PHE   0.017   0.001   PHE A1068 
 TYR   0.037   0.001   TYR A1181 
 ARG   0.005   0.000   ARG A1114 

Details of bonding type rmsd
  link_TRANS           : bond        0.00000 (    1)
  link_TRANS           : angle       0.30389 (    3)
  link_NAG-ASN         : bond        0.00416 (    6)
  link_NAG-ASN         : angle       2.96176 (   18)
  link_BETA1-4         : bond        0.00130 (    1)
  link_BETA1-4         : angle       2.57437 (    3)
  hydrogen bonds       : bond        0.03698 (  423)
  hydrogen bonds       : angle       4.19820 ( 1236)
  metal coordination   : bond        0.00164 (    2)
  SS BOND              : bond        0.00130 (    3)
  SS BOND              : angle       1.09167 (    6)
  covalent geometry    : bond        0.00273 ( 9432)
  covalent geometry    : angle       0.74268 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 137
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 LEU cc_start: 0.6701 (OUTLIER) cc_final: 0.6474 (pt)
REVERT: A  397 GLU cc_start: 0.7479 (pp20) cc_final: 0.7141 (pp20)
REVERT: A  422 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7404 (p90)
REVERT: A  750 LYS cc_start: 0.6653 (mmpt) cc_final: 0.6126 (pttt)
REVERT: A  770 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.6342 (mtt180)
REVERT: A  981 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7108 (pp)
REVERT: A 1051 TRP cc_start: 0.6411 (t-100) cc_final: 0.5474 (m-10)
REVERT: A 1055 ILE cc_start: 0.8112 (mm) cc_final: 0.7882 (mt)
REVERT: B  177 SER cc_start: 0.8852 (t) cc_final: 0.8372 (t)
  outliers start: 47
  outliers final: 32
  residues processed: 174
  average time/residue: 0.1826
  time to fit residues: 46.4137
Evaluate side-chains
  164 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 128
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  129 TRP
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 PHE
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  289 HIS
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  770 ARG
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  900 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1058 MET
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain B residue  166 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 61 optimal weight:    0.3980
   chunk 59 optimal weight:    0.2980
   chunk 31 optimal weight:    6.9990
   chunk 67 optimal weight:    0.0270
   chunk 36 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 72 optimal weight:    0.4980
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
A 358 HIS
A 361 GLN
** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.140663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.125186 restraints weight = 18677.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.127731 restraints weight = 10485.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.129338 restraints weight = 7181.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.5899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9445  Z= 0.129
  Angle     :  0.764  13.060  12855  Z= 0.369
  Chirality :  0.045   0.243   1471
  Planarity :  0.005   0.052   1601
  Dihedral  :  7.150  59.943   1534
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.29 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 23.34 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    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: -0.62 (0.26), residues: 1137
  helix:  0.86 (0.21), residues: 632
  sheet: -0.59 (0.60), residues: 67
  loop : -2.36 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 844 
 HIS   0.004   0.001   HIS A1099 
 PHE   0.014   0.001   PHE A1068 
 TYR   0.037   0.001   TYR A1181 
 ARG   0.005   0.000   ARG A1114 

Details of bonding type rmsd
  link_TRANS           : bond        0.00045 (    1)
  link_TRANS           : angle       0.22045 (    3)
  link_NAG-ASN         : bond        0.00395 (    6)
  link_NAG-ASN         : angle       2.86217 (   18)
  link_BETA1-4         : bond        0.00077 (    1)
  link_BETA1-4         : angle       2.37104 (    3)
  hydrogen bonds       : bond        0.03586 (  423)
  hydrogen bonds       : angle       4.16805 ( 1236)
  metal coordination   : bond        0.00116 (    2)
  SS BOND              : bond        0.00117 (    3)
  SS BOND              : angle       1.11199 (    6)
  covalent geometry    : bond        0.00274 ( 9432)
  covalent geometry    : angle       0.75622 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 143
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   86 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6471 (pt)
REVERT: A  397 GLU cc_start: 0.7393 (pp20) cc_final: 0.7073 (pp20)
REVERT: A  422 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7434 (p90)
REVERT: A  750 LYS cc_start: 0.6649 (mmpt) cc_final: 0.6169 (pttt)
REVERT: A  756 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7396 (mt)
REVERT: A  770 ARG cc_start: 0.6577 (OUTLIER) cc_final: 0.6358 (mtt180)
REVERT: A  956 MET cc_start: 0.7478 (ppp) cc_final: 0.6509 (mmt)
REVERT: A  981 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6992 (pp)
REVERT: A 1051 TRP cc_start: 0.6315 (t-100) cc_final: 0.5417 (m-10)
REVERT: A 1055 ILE cc_start: 0.8129 (mm) cc_final: 0.7913 (mt)
REVERT: B  172 TRP cc_start: 0.8722 (OUTLIER) cc_final: 0.8365 (t60)
REVERT: B  177 SER cc_start: 0.8764 (t) cc_final: 0.8261 (t)
  outliers start: 44
  outliers final: 33
  residues processed: 176
  average time/residue: 0.1735
  time to fit residues: 46.0846
Evaluate side-chains
  171 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 132
  time to evaluate  : 0.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  129 TRP
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  259 PHE
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  289 HIS
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  770 ARG
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  900 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  172 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 110 optimal weight:    0.0060
   chunk 32 optimal weight:    0.9980
   chunk 66 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.9998

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN
** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.141253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.125943 restraints weight = 18963.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.128475 restraints weight = 10729.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.130063 restraints weight = 7344.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.6020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   9445  Z= 0.138
  Angle     :  0.771  12.435  12855  Z= 0.373
  Chirality :  0.045   0.245   1471
  Planarity :  0.005   0.054   1601
  Dihedral  :  7.125  59.142   1534
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.03 %
    Favored  : 89.89 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 23.96 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.26), residues: 1137
  helix:  0.92 (0.21), residues: 632
  sheet: -0.53 (0.59), residues: 67
  loop : -2.31 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 844 
 HIS   0.003   0.001   HIS A1099 
 PHE   0.016   0.001   PHE A 848 
 TYR   0.035   0.001   TYR A1181 
 ARG   0.004   0.000   ARG A1114 

Details of bonding type rmsd
  link_TRANS           : bond        0.00005 (    1)
  link_TRANS           : angle       0.35755 (    3)
  link_NAG-ASN         : bond        0.00379 (    6)
  link_NAG-ASN         : angle       2.84934 (   18)
  link_BETA1-4         : bond        0.00015 (    1)
  link_BETA1-4         : angle       2.48746 (    3)
  hydrogen bonds       : bond        0.03653 (  423)
  hydrogen bonds       : angle       4.16820 ( 1236)
  metal coordination   : bond        0.00313 (    2)
  SS BOND              : bond        0.00126 (    3)
  SS BOND              : angle       1.13092 (    6)
  covalent geometry    : bond        0.00306 ( 9432)
  covalent geometry    : angle       0.76354 (12825)

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

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

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2274 Ramachandran restraints generated.
    1137 Oldfield, 0 Emsley, 1137 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 132
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 GLU cc_start: 0.7432 (pp20) cc_final: 0.7134 (pp20)
REVERT: A  422 PHE cc_start: 0.7830 (OUTLIER) cc_final: 0.7459 (p90)
REVERT: A  501 GLN cc_start: 0.8307 (mp10) cc_final: 0.7793 (mp10)
REVERT: A  750 LYS cc_start: 0.6719 (mmpt) cc_final: 0.6234 (pttt)
REVERT: A  756 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7390 (mt)
REVERT: A  770 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6402 (mtt180)
REVERT: A  981 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7097 (pp)
REVERT: A 1051 TRP cc_start: 0.6204 (t-100) cc_final: 0.5368 (m-10)
REVERT: A 1055 ILE cc_start: 0.8112 (mm) cc_final: 0.7892 (mt)
REVERT: B  172 TRP cc_start: 0.8707 (OUTLIER) cc_final: 0.8372 (t60)
REVERT: B  177 SER cc_start: 0.8821 (t) cc_final: 0.8467 (t)
  outliers start: 41
  outliers final: 33
  residues processed: 163
  average time/residue: 0.1790
  time to fit residues: 43.6467
Evaluate side-chains
  168 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 130
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  129 TRP
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  232 LEU
Chi-restraints excluded: chain A residue  259 PHE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  287 VAL
Chi-restraints excluded: chain A residue  289 HIS
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  323 LEU
Chi-restraints excluded: chain A residue  361 GLN
Chi-restraints excluded: chain A residue  422 PHE
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  476 LEU
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  756 LEU
Chi-restraints excluded: chain A residue  770 ARG
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  806 VAL
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  867 LYS
Chi-restraints excluded: chain A residue  900 SER
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue  914 ILE
Chi-restraints excluded: chain A residue  981 LEU
Chi-restraints excluded: chain A residue 1029 LEU
Chi-restraints excluded: chain A residue 1030 LEU
Chi-restraints excluded: chain A residue 1043 CYS
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain B residue  166 VAL
Chi-restraints excluded: chain B residue  172 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 57 optimal weight:    7.9990
   chunk 100 optimal weight:    7.9990
   chunk 90 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 64 optimal weight:    0.0040
   chunk 104 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   overall best weight:    1.7998

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

Flipped N/Q/H residues before XYZ refinement:
A 361 GLN
** A 979 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.137352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.122026 restraints weight = 18881.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.124523 restraints weight = 10715.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.126083 restraints weight = 7372.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.6117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   9445  Z= 0.170
  Angle     :  0.801  11.436  12855  Z= 0.390
  Chirality :  0.047   0.252   1471
  Planarity :  0.005   0.057   1601
  Dihedral  :  7.316  59.509   1534
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.35 %
    Favored  : 88.57 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 24.17 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.17 %
    Cis-general     : 0.09 %
    Twisted Proline : 2.08 %
    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: -0.52 (0.26), residues: 1137
  helix:  0.93 (0.21), residues: 630
  sheet: -0.63 (0.58), residues: 67
  loop : -2.26 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 460 
 HIS   0.005   0.001   HIS A1099 
 PHE   0.023   0.002   PHE A 848 
 TYR   0.035   0.002   TYR A1181 
 ARG   0.004   0.001   ARG B 101 

Details of bonding type rmsd
  link_TRANS           : bond        0.00103 (    1)
  link_TRANS           : angle       0.39655 (    3)
  link_NAG-ASN         : bond        0.00409 (    6)
  link_NAG-ASN         : angle       2.92203 (   18)
  link_BETA1-4         : bond        0.00209 (    1)
  link_BETA1-4         : angle       2.97250 (    3)
  hydrogen bonds       : bond        0.04102 (  423)
  hydrogen bonds       : angle       4.32286 ( 1236)
  metal coordination   : bond        0.00481 (    2)
  SS BOND              : bond        0.00172 (    3)
  SS BOND              : angle       1.18700 (    6)
  covalent geometry    : bond        0.00393 ( 9432)
  covalent geometry    : angle       0.79277 (12825)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3110.80 seconds
wall clock time: 54 minutes 36.22 seconds (3276.22 seconds total)