Starting phenix.real_space_refine
on Wed Mar  4 13:07:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qds_13925/03_2026/7qds_13925.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qds_13925/03_2026/7qds_13925.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qds_13925/03_2026/7qds_13925.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qds_13925/03_2026/7qds_13925.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qds_13925/03_2026/7qds_13925.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qds_13925/03_2026/7qds_13925.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    8774      2.51       5
     N    2355      2.21       5
     O    2609      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 82 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13798
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1192
          Classifications: {'peptide': 155}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 20, 'TRANS': 134}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 7860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1006, 7860
          Classifications: {'peptide': 1006}
          Link IDs: {'PTRANS': 24, 'TRANS': 981}
    Chain: "C"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2373
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 8, 'TRANS': 296}
    Chain: "D"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2373
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 8, 'TRANS': 296}
  Time building chain proxies: 2.70, per 1000 atoms: 0.20
  Number of scatterers: 13798
  At special positions: 0
  Unit cell: (145.502, 117.058, 122.528, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    2609      8.00
     N    2355      7.00
     C    8774      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 481.7 milliseconds
  

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3320

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 18 sheets defined
      48.6% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 64
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.813A  pdb=" N   GLY A  73 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.578A  pdb=" N   LEU A  90 " --> pdb=" O   PRO A  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 577
      removed outlier: 3.548A  pdb=" N   ARG B 569 " --> pdb=" O   TRP B 565 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA B 577 " --> pdb=" O   TYR B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 579 through 594
    Processing helix  chain 'B' and resid 597 through 611
      removed outlier: 3.616A  pdb=" N   ARG B 611 " --> pdb=" O   ALA B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 614 through 627
      removed outlier: 3.988A  pdb=" N   LEU B 627 " --> pdb=" O   LYS B 623 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 645
      removed outlier: 3.627A  pdb=" N   VAL B 635 " --> pdb=" O   SER B 631 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU B 645 " --> pdb=" O   ILE B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 662
      removed outlier: 3.695A  pdb=" N   ALA B 651 " --> pdb=" O   LYS B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 686
      removed outlier: 3.580A  pdb=" N   ASP B 686 " --> pdb=" O   ALA B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 710
      removed outlier: 3.936A  pdb=" N   HIS B 709 " --> pdb=" O   CYS B 705 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG B 710 " --> pdb=" O   ALA B 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 726
      removed outlier: 4.302A  pdb=" N   TRP B 717 " --> pdb=" O   VAL B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 741 through 745
      removed outlier: 3.586A  pdb=" N   LEU B 744 " --> pdb=" O   GLY B 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 754 through 773
      removed outlier: 3.954A  pdb=" N   LEU B 772 " --> pdb=" O   ARG B 768 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   MET B 773 " --> pdb=" O   ALA B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 796
    Processing helix  chain 'B' and resid 803 through 821
    Processing helix  chain 'B' and resid 824 through 836
      removed outlier: 3.731A  pdb=" N   TRP B 828 " --> pdb=" O   ASN B 824 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS B 836 " --> pdb=" O   GLY B 832 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 857
    Processing helix  chain 'B' and resid 860 through 874
      removed outlier: 3.819A  pdb=" N   TRP B 864 " --> pdb=" O   ASN B 860 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 876 through 891
    Processing helix  chain 'B' and resid 894 through 908
      removed outlier: 3.915A  pdb=" N   TRP B 898 " --> pdb=" O   TYR B 894 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 912 through 925
      removed outlier: 3.610A  pdb=" N   ASN B 924 " --> pdb=" O   THR B 920 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   MET B 925 " --> pdb=" O   THR B 921 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 926 through 943
    Processing helix  chain 'B' and resid 951 through 960
    Processing helix  chain 'B' and resid 960 through 976
      removed outlier: 3.613A  pdb=" N   ALA B 964 " --> pdb=" O   ASN B 960 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 979 through 993
      removed outlier: 3.803A  pdb=" N   PHE B 983 " --> pdb=" O   TYR B 979 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 995 through 1011
      removed outlier: 3.506A  pdb=" N   ALA B 999 " --> pdb=" O   LEU B 995 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1019 through 1033
      removed outlier: 3.591A  pdb=" N   THR B1033 " --> pdb=" O   LEU B1029 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1035 through 1045
    Processing helix  chain 'B' and resid 1050 through 1065
    Processing helix  chain 'B' and resid 1066 through 1080
      removed outlier: 3.738A  pdb=" N   ILE B1080 " --> pdb=" O   ARG B1076 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1084 through 1101
      removed outlier: 3.853A  pdb=" N   GLN B1101 " --> pdb=" O   THR B1097 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1103 through 1116
      removed outlier: 3.746A  pdb=" N   ALA B1107 " --> pdb=" O   LYS B1103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1123 through 1134
    Processing helix  chain 'B' and resid 1139 through 1152
      removed outlier: 3.813A  pdb=" N   HIS B1151 " --> pdb=" O   GLU B1147 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE B1152 " --> pdb=" O   LEU B1148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1159 through 1172
      removed outlier: 3.724A  pdb=" N   GLN B1172 " --> pdb=" O   ILE B1168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1176 through 1189
      removed outlier: 3.557A  pdb=" N   LYS B1180 " --> pdb=" O   VAL B1176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1192 through 1206
      removed outlier: 3.853A  pdb=" N   TRP B1196 " --> pdb=" O   ASP B1192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1210 through 1224
    Processing helix  chain 'B' and resid 1228 through 1244
    Processing helix  chain 'B' and resid 1254 through 1266
    Processing helix  chain 'B' and resid 1269 through 1291
      removed outlier: 4.494A  pdb=" N   TRP B1273 " --> pdb=" O   ASP B1269 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA B1274 " --> pdb=" O   PRO B1270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1299 through 1313
      removed outlier: 4.126A  pdb=" N   ASP B1313 " --> pdb=" O   ALA B1309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1317 through 1340
    Processing helix  chain 'B' and resid 1341 through 1356
      removed outlier: 3.648A  pdb=" N   ASN B1356 " --> pdb=" O   ASN B1352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1359 through 1371
      removed outlier: 3.715A  pdb=" N   ILE B1363 " --> pdb=" O   GLN B1359 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LEU B1364 " --> pdb=" O   PRO B1360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1382 through 1396
    Processing helix  chain 'B' and resid 1399 through 1414
      removed outlier: 3.844A  pdb=" N   TRP B1403 " --> pdb=" O   SER B1399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1415 through 1434
    Processing helix  chain 'B' and resid 1436 through 1456
      removed outlier: 4.028A  pdb=" N   ALA B1456 " --> pdb=" O   LYS B1452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1462 through 1478
    Processing helix  chain 'B' and resid 1480 through 1494
    Processing helix  chain 'B' and resid 1499 through 1511
    Processing helix  chain 'B' and resid 1515 through 1533
    Processing helix  chain 'B' and resid 1535 through 1548
    Processing helix  chain 'B' and resid 1552 through 1563
      removed outlier: 4.089A  pdb=" N   SER B1563 " --> pdb=" O   GLN B1559 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
    Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104
    Processing sheet with id=AA3, first strand: chain 'B' and resid 737 through 739
    Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 11
      removed outlier: 7.039A  pdb=" N   ILE C 300 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   LYS C  10 " --> pdb=" O   ILE C 298 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ILE C 298 " --> pdb=" O   LYS C  10 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 25
      removed outlier: 6.563A  pdb=" N   VAL C  46 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 72
      removed outlier: 3.515A  pdb=" N   SER C  69 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA C  79 " --> pdb=" O   TRP C  91 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 113
      removed outlier: 3.752A  pdb=" N   TYR C 142 " --> pdb=" O   ILE C 132 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   GLY C 134 " --> pdb=" O   LYS C 140 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   LYS C 140 " --> pdb=" O   GLY C 134 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 151 through 156
      removed outlier: 6.630A  pdb=" N   GLY C 166 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ILE C 154 " --> pdb=" O   ALA C 164 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ALA C 164 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE C 174 " --> pdb=" O   HIS C 184 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   HIS C 184 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 196 through 198
    Processing sheet with id=AB1, first strand: chain 'C' and resid 213 through 217
      removed outlier: 6.073A  pdb=" N   ILE C 214 " --> pdb=" O   THR C 227 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR C 227 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ILE C 216 " --> pdb=" O   ALA C 225 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 235 through 240
      removed outlier: 3.550A  pdb=" N   ASN C 237 " --> pdb=" O   SER C 250 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   HIS C 268 " --> pdb=" O   VAL C 258 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ASP C 260 " --> pdb=" O   CYS C 266 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   CYS C 266 " --> pdb=" O   ASP C 260 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 21 through 25
      removed outlier: 3.714A  pdb=" N   TRP D  58 " --> pdb=" O   VAL D  46 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LYS D  48 " --> pdb=" O   LEU D  56 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   LEU D  56 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 67 through 72
      removed outlier: 3.506A  pdb=" N   SER D  69 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS D 100 " --> pdb=" O   LEU D  90 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 113
    Processing sheet with id=AB6, first strand: chain 'D' and resid 163 through 166
      removed outlier: 3.825A  pdb=" N   ILE D 174 " --> pdb=" O   HIS D 184 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   HIS D 184 " --> pdb=" O   ILE D 174 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 195 through 197
      removed outlier: 4.569A  pdb=" N   SER D 195 " --> pdb=" O   ALA D 208 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE D 216 " --> pdb=" O   GLY D 226 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY D 226 " --> pdb=" O   ILE D 216 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 235 through 239
      removed outlier: 6.835A  pdb=" N   SER D 250 " --> pdb=" O   LEU D 236 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   VAL D 238 " --> pdb=" O   VAL D 248 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL D 248 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   SER D 255 " --> pdb=" O   SER D 251 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   VAL D 256 " --> pdb=" O   PHE D 270 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   HIS D 268 " --> pdb=" O   VAL D 258 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   ASP D 260 " --> pdb=" O   CYS D 266 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   CYS D 266 " --> pdb=" O   ASP D 260 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 277 through 282

    714 hydrogen bonds defined for protein.
    2067 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: 2.42

  Time building geometry restraints manager: 1.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4467
        1.34 -     1.46: 2215
        1.46 -     1.58: 7327
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 14097
  Sorted by residual:
  bond pdb=" CB  VAL D 290 "
       pdb=" CG2 VAL D 290 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.85e+00
  bond pdb=" CB  ILE B 968 "
       pdb=" CG2 ILE B 968 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.35e+00
  bond pdb=" CB  GLU A  31 "
       pdb=" CG  GLU A  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.479  0.041 3.00e-02 1.11e+03 1.87e+00
  bond pdb=" CB  CYS B 715 "
       pdb=" SG  CYS B 715 "
    ideal  model  delta    sigma   weight residual
    1.808  1.767  0.041 3.30e-02 9.18e+02 1.52e+00
  bond pdb=" CG1 ILE B1007 "
       pdb=" CD1 ILE B1007 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.29e+00
  ... (remaining 14092 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.48: 18961
        3.48 -     6.97: 166
        6.97 -    10.45: 11
       10.45 -    13.93: 2
       13.93 -    17.42: 1
  Bond angle restraints: 19141
  Sorted by residual:
  angle pdb=" C   GLU A  31 "
        pdb=" CA  GLU A  31 "
        pdb=" CB  GLU A  31 "
      ideal   model   delta    sigma   weight residual
     110.67  120.27   -9.60 2.23e+00 2.01e-01 1.85e+01
  angle pdb=" CA  LEU A  43 "
        pdb=" CB  LEU A  43 "
        pdb=" CG  LEU A  43 "
      ideal   model   delta    sigma   weight residual
     116.30  129.46  -13.16 3.50e+00 8.16e-02 1.41e+01
  angle pdb=" CB  MET A 194 "
        pdb=" CG  MET A 194 "
        pdb=" SD  MET A 194 "
      ideal   model   delta    sigma   weight residual
     112.70  101.54   11.16 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" C   GLU B1014 "
        pdb=" N   ASP B1015 "
        pdb=" CA  ASP B1015 "
      ideal   model   delta    sigma   weight residual
     125.66  132.08   -6.42 1.85e+00 2.92e-01 1.20e+01
  angle pdb=" N   GLU A  31 "
        pdb=" CA  GLU A  31 "
        pdb=" CB  GLU A  31 "
      ideal   model   delta    sigma   weight residual
     111.62  106.47    5.15 1.62e+00 3.81e-01 1.01e+01
  ... (remaining 19136 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 7445
       17.33 -    34.65: 816
       34.65 -    51.98: 112
       51.98 -    69.31: 22
       69.31 -    86.63: 18
  Dihedral angle restraints: 8413
    sinusoidal: 3260
      harmonic: 5153
  Sorted by residual:
  dihedral pdb=" CA  ASP D 201 "
           pdb=" C   ASP D 201 "
           pdb=" N   SER D 202 "
           pdb=" CA  SER D 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.83  -27.17     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  ARG B 947 "
           pdb=" C   ARG B 947 "
           pdb=" N   GLU B 948 "
           pdb=" CA  GLU B 948 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.25   25.75     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  GLY D  38 "
           pdb=" C   GLY D  38 "
           pdb=" N   SER D  39 "
           pdb=" CA  SER D  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.56  -25.44     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 8410 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1406
       0.042 -    0.084: 557
       0.084 -    0.125: 161
       0.125 -    0.167: 32
       0.167 -    0.209: 6
  Chirality restraints: 2162
  Sorted by residual:
  chirality pdb=" CB  ILE D 151 "
            pdb=" CA  ILE D 151 "
            pdb=" CG1 ILE D 151 "
            pdb=" CG2 ILE D 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  GLU A  31 "
            pdb=" N   GLU A  31 "
            pdb=" C   GLU A  31 "
            pdb=" CB  GLU A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.05e-01
  chirality pdb=" CA  ASN B1396 "
            pdb=" N   ASN B1396 "
            pdb=" C   ASN B1396 "
            pdb=" CB  ASN B1396 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.67e-01
  ... (remaining 2159 not shown)

  Planarity restraints: 2434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B1119 "    0.092 5.00e-02 4.00e+02   1.39e-01 3.07e+01
        pdb=" N   PRO B1120 "   -0.240 5.00e-02 4.00e+02
        pdb=" CA  PRO B1120 "    0.076 5.00e-02 4.00e+02
        pdb=" CD  PRO B1120 "    0.071 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 105 "   -0.048 5.00e-02 4.00e+02   7.37e-02 8.70e+00
        pdb=" N   PRO C 106 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO C 106 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C 106 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B1256 "    0.015 2.00e-02 2.50e+03   2.90e-02 8.43e+00
        pdb=" C   LEU B1256 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LEU B1256 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LYS B1257 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2431 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 207
        2.63 -     3.20: 13015
        3.20 -     3.77: 20682
        3.77 -     4.33: 27067
        4.33 -     4.90: 46078
  Nonbonded interactions: 107049
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 251 "
            pdb=" OD1 ASP C 253 "
     model   vdw
     2.067 3.040
  nonbonded pdb=" OE2 GLU B1314 "
            pdb=" ND2 ASN B1321 "
     model   vdw
     2.094 3.120
  nonbonded pdb=" OG  SER B1157 "
            pdb=" OE1 GLN B1160 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" OD1 ASP D 253 "
            pdb=" OG  SER D 255 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OE1 GLN B 588 "
            pdb=" OH  TYR B 608 "
     model   vdw
     2.188 3.040
  ... (remaining 107044 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:             3.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     11.990
  Find NCS groups from input model:        0.090
  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:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
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      :  0.005   0.056  14097  Z= 0.202
  Angle     :  0.856  17.416  19141  Z= 0.456
  Chirality :  0.049   0.209   2162
  Planarity :  0.006   0.139   2434
  Dihedral  : 14.594  86.633   5093
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.33 (0.21), residues: 1761
  helix:  2.76 (0.18), residues: 806
  sheet: -1.96 (0.31), residues: 250
  loop : -3.37 (0.18), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B1553 
 TYR   0.034   0.002   TYR D 156 
 PHE   0.029   0.003   PHE D 240 
 TRP   0.034   0.002   TRP B 936 
 HIS   0.013   0.002   HIS B 992 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (14097)
  covalent geometry    : angle       0.85647 (19141)
  hydrogen bonds       : bond        0.13418 (  714)
  hydrogen bonds       : angle       5.45123 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A  192 LYS cc_start: 0.8440 (mttt) cc_final: 0.8177 (tttp)
REVERT: B 1118 LYS cc_start: 0.7763 (pptt) cc_final: 0.7221 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.0896
  time to fit residues: 16.8916
Evaluate side-chains
  82 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.1980
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 588 GLN
** C 299 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 = 0.3659 r_free = 0.3659 target = 0.113367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.087945 restraints weight = 27901.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.088511 restraints weight = 20051.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.089533 restraints weight = 15916.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.090239 restraints weight = 13918.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.090385 restraints weight = 11959.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14097  Z= 0.144
  Angle     :  0.677  12.383  19141  Z= 0.349
  Chirality :  0.043   0.168   2162
  Planarity :  0.005   0.079   2434
  Dihedral  :  5.187  24.728   1886
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.78 %
    Favored  : 89.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.21), residues: 1761
  helix:  2.53 (0.18), residues: 828
  sheet: -1.65 (0.33), residues: 248
  loop : -3.14 (0.19), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B1005 
 TYR   0.018   0.001   TYR B 935 
 PHE   0.022   0.002   PHE D 240 
 TRP   0.016   0.001   TRP B 936 
 HIS   0.004   0.001   HIS B1187 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (14097)
  covalent geometry    : angle       0.67650 (19141)
  hydrogen bonds       : bond        0.04587 (  714)
  hydrogen bonds       : angle       4.33975 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 LYS cc_start: 0.8385 (mttt) cc_final: 0.8182 (tttp)
REVERT: B 1118 LYS cc_start: 0.7732 (pptt) cc_final: 0.7066 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.8032 (t0)
  outliers start: 14
  outliers final: 5
  residues processed: 123
  average time/residue: 0.1054
  time to fit residues: 20.1083
Evaluate side-chains
  92 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain D residue  201 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 156 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 106 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 165 optimal weight:    1.9990
   chunk 92 optimal weight:    0.8980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 642 GLN
B 942 GLN
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1321 ASN
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1413 GLN ** 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 = 0.3593 r_free = 0.3593 target = 0.109044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.083829 restraints weight = 28312.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.085099 restraints weight = 20944.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.085793 restraints weight = 16741.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.086233 restraints weight = 14462.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.086455 restraints weight = 13559.255|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14097  Z= 0.204
  Angle     :  0.686  12.403  19141  Z= 0.358
  Chirality :  0.044   0.175   2162
  Planarity :  0.005   0.058   2434
  Dihedral  :  5.229  26.205   1886
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.75 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.31 (0.21), residues: 1761
  helix:  2.37 (0.18), residues: 826
  sheet: -1.59 (0.33), residues: 266
  loop : -3.13 (0.20), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B1005 
 TYR   0.016   0.002   TYR B 935 
 PHE   0.025   0.002   PHE B1316 
 TRP   0.017   0.002   TRP B 936 
 HIS   0.004   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (14097)
  covalent geometry    : angle       0.68599 (19141)
  hydrogen bonds       : bond        0.04901 (  714)
  hydrogen bonds       : angle       4.23649 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.444 
Fit side-chains
REVERT: B 1383 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7990 (t0)
REVERT: D   94 GLU cc_start: 0.7805 (tp30) cc_final: 0.7480 (tp30)
  outliers start: 33
  outliers final: 18
  residues processed: 131
  average time/residue: 0.0920
  time to fit residues: 19.2497
Evaluate side-chains
  109 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain D residue  153 SER
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 122 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 165 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 151 optimal weight:    0.7980
   chunk 89 optimal weight:    0.9980
   chunk 123 optimal weight:    0.9980
   chunk 133 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.110036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.085247 restraints weight = 27853.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.085565 restraints weight = 22298.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.086746 restraints weight = 18101.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.087167 restraints weight = 14600.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.087339 restraints weight = 13237.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14097  Z= 0.152
  Angle     :  0.630  15.322  19141  Z= 0.325
  Chirality :  0.042   0.169   2162
  Planarity :  0.004   0.051   2434
  Dihedral  :  5.042  23.579   1886
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.44 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.21), residues: 1761
  helix:  2.39 (0.18), residues: 829
  sheet: -1.46 (0.33), residues: 272
  loop : -3.04 (0.20), residues: 660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B1005 
 TYR   0.014   0.001   TYR B 935 
 PHE   0.015   0.002   PHE D 150 
 TRP   0.021   0.001   TRP D  47 
 HIS   0.004   0.001   HIS D  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (14097)
  covalent geometry    : angle       0.62977 (19141)
  hydrogen bonds       : bond        0.04228 (  714)
  hydrogen bonds       : angle       4.02734 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 103
  time to evaluate  : 0.549 
Fit side-chains
REVERT: B 1118 LYS cc_start: 0.7574 (pptt) cc_final: 0.6812 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8023 (t0)
REVERT: B 1504 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7969 (tp)
REVERT: D   94 GLU cc_start: 0.7828 (tp30) cc_final: 0.7515 (tp30)
  outliers start: 40
  outliers final: 24
  residues processed: 138
  average time/residue: 0.0945
  time to fit residues: 21.1240
Evaluate side-chains
  119 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  722 ASP
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1098 GLU
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1504 LEU
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 14 optimal weight:    0.0170
   chunk 6 optimal weight:    0.0980
   chunk 78 optimal weight:    0.8980
   chunk 151 optimal weight:    0.4980
   chunk 132 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 154 optimal weight:    0.6980
   chunk 106 optimal weight:    0.6980
   chunk 163 optimal weight:    5.9990
   chunk 130 optimal weight:    0.5980
   overall best weight:    0.3818

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

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.112469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.086414 restraints weight = 28036.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.087769 restraints weight = 20674.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.088750 restraints weight = 15881.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.089024 restraints weight = 13343.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.089252 restraints weight = 12717.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  14097  Z= 0.115
  Angle     :  0.595  12.551  19141  Z= 0.306
  Chirality :  0.041   0.165   2162
  Planarity :  0.004   0.049   2434
  Dihedral  :  4.774  23.304   1886
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.53 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.21), residues: 1761
  helix:  2.47 (0.18), residues: 830
  sheet: -1.22 (0.34), residues: 262
  loop : -2.92 (0.20), residues: 669

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 611 
 TYR   0.011   0.001   TYR B 935 
 PHE   0.027   0.001   PHE B1316 
 TRP   0.020   0.001   TRP D  47 
 HIS   0.004   0.001   HIS D 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (14097)
  covalent geometry    : angle       0.59506 (19141)
  hydrogen bonds       : bond        0.03555 (  714)
  hydrogen bonds       : angle       3.78336 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 110
  time to evaluate  : 0.514 
Fit side-chains
REVERT: B 1101 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7911 (mt0)
REVERT: B 1118 LYS cc_start: 0.7598 (pptt) cc_final: 0.6719 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8010 (t0)
REVERT: B 1504 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7988 (tp)
REVERT: D   94 GLU cc_start: 0.7845 (tp30) cc_final: 0.7516 (tp30)
  outliers start: 34
  outliers final: 19
  residues processed: 140
  average time/residue: 0.0934
  time to fit residues: 20.6182
Evaluate side-chains
  116 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1101 GLN
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1504 LEU
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  153 SER
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 133 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 35 optimal weight:    0.6980
   chunk 169 optimal weight:    0.9990
   chunk 134 optimal weight:    0.9980
   chunk 55 optimal weight:    0.4980
   chunk 79 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1491 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.110594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.085023 restraints weight = 27840.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.086383 restraints weight = 19328.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.087418 restraints weight = 15017.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.087659 restraints weight = 13074.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.087969 restraints weight = 11900.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14097  Z= 0.142
  Angle     :  0.609  11.915  19141  Z= 0.314
  Chirality :  0.041   0.166   2162
  Planarity :  0.004   0.048   2434
  Dihedral  :  4.754  23.134   1886
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 16.80 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.21), residues: 1761
  helix:  2.49 (0.18), residues: 829
  sheet: -1.25 (0.34), residues: 256
  loop : -2.94 (0.20), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  53 
 TYR   0.011   0.001   TYR B 935 
 PHE   0.014   0.001   PHE D 150 
 TRP   0.020   0.001   TRP D  47 
 HIS   0.004   0.001   HIS C 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14097)
  covalent geometry    : angle       0.60931 (19141)
  hydrogen bonds       : bond        0.03864 (  714)
  hydrogen bonds       : angle       3.77414 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 95
  time to evaluate  : 0.425 
Fit side-chains
REVERT: B  773 MET cc_start: 0.8129 (mmm) cc_final: 0.7777 (mmm)
REVERT: B 1101 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.8018 (mt0)
REVERT: B 1118 LYS cc_start: 0.7612 (pptt) cc_final: 0.6747 (mmtt)
REVERT: B 1160 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.8122 (mp10)
REVERT: B 1383 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7997 (t0)
REVERT: B 1506 GLU cc_start: 0.8212 (pt0) cc_final: 0.7961 (pt0)
REVERT: D   94 GLU cc_start: 0.7845 (tp30) cc_final: 0.7515 (tp30)
REVERT: D  156 TYR cc_start: 0.8176 (OUTLIER) cc_final: 0.7399 (t80)
  outliers start: 45
  outliers final: 27
  residues processed: 137
  average time/residue: 0.0892
  time to fit residues: 19.8576
Evaluate side-chains
  120 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 89
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1050 VAL
Chi-restraints excluded: chain B residue 1101 GLN
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1176 VAL
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  153 SER
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 153 optimal weight:    2.9990
   chunk 77 optimal weight:    0.5980
   chunk 112 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 73 optimal weight:    0.1980
   chunk 103 optimal weight:    0.9990
   chunk 149 optimal weight:    0.7980
   chunk 107 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.110793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.085002 restraints weight = 28013.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.085836 restraints weight = 21049.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.086723 restraints weight = 17003.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.088166 restraints weight = 13583.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.088125 restraints weight = 12317.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14097  Z= 0.130
  Angle     :  0.597  11.493  19141  Z= 0.308
  Chirality :  0.041   0.165   2162
  Planarity :  0.004   0.048   2434
  Dihedral  :  4.687  22.366   1886
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.37 %
    Favored  : 90.63 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 17.41 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.21), residues: 1761
  helix:  2.50 (0.18), residues: 829
  sheet: -1.17 (0.34), residues: 254
  loop : -2.90 (0.20), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  53 
 TYR   0.010   0.001   TYR B 935 
 PHE   0.031   0.001   PHE B1316 
 TRP   0.022   0.001   TRP D  47 
 HIS   0.005   0.001   HIS C 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (14097)
  covalent geometry    : angle       0.59749 (19141)
  hydrogen bonds       : bond        0.03678 (  714)
  hydrogen bonds       : angle       3.69200 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 96
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7373 (pt)
REVERT: B  773 MET cc_start: 0.8198 (mmm) cc_final: 0.7923 (mmm)
REVERT: B  800 MET cc_start: 0.5965 (tpt) cc_final: 0.5410 (mmp)
REVERT: B 1101 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8027 (mt0)
REVERT: B 1118 LYS cc_start: 0.7509 (pptt) cc_final: 0.6682 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8050 (t0)
REVERT: B 1415 MET cc_start: 0.7342 (mmm) cc_final: 0.6841 (tpp)
REVERT: D   94 GLU cc_start: 0.7802 (tp30) cc_final: 0.7506 (tp30)
REVERT: D  156 TYR cc_start: 0.8148 (OUTLIER) cc_final: 0.7378 (t80)
  outliers start: 39
  outliers final: 29
  residues processed: 129
  average time/residue: 0.0931
  time to fit residues: 19.7971
Evaluate side-chains
  124 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 91
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1050 VAL
Chi-restraints excluded: chain B residue 1101 GLN
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1176 VAL
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1286 LEU
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1562 SER
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  153 SER
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 90 optimal weight:    0.1980
   chunk 100 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0670
   chunk 85 optimal weight:    0.9980
   chunk 144 optimal weight:    2.9990
   chunk 11 optimal weight:    8.9990
   chunk 40 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 157 optimal weight:    0.0980
   chunk 141 optimal weight:    1.9990
   overall best weight:    0.4720

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

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.111894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.086894 restraints weight = 27914.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.087485 restraints weight = 21173.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.087911 restraints weight = 18554.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.088627 restraints weight = 16106.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.088681 restraints weight = 14207.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14097  Z= 0.117
  Angle     :  0.587  10.920  19141  Z= 0.302
  Chirality :  0.040   0.164   2162
  Planarity :  0.004   0.049   2434
  Dihedral  :  4.575  23.151   1886
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 18.42 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.21), residues: 1761
  helix:  2.53 (0.18), residues: 829
  sheet: -1.08 (0.34), residues: 249
  loop : -2.85 (0.20), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 611 
 TYR   0.011   0.001   TYR B1536 
 PHE   0.012   0.001   PHE D 150 
 TRP   0.022   0.001   TRP D  47 
 HIS   0.006   0.001   HIS D  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (14097)
  covalent geometry    : angle       0.58689 (19141)
  hydrogen bonds       : bond        0.03424 (  714)
  hydrogen bonds       : angle       3.63614 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
REVERT: B  773 MET cc_start: 0.8227 (mmm) cc_final: 0.7929 (mmm)
REVERT: B  800 MET cc_start: 0.5960 (tpt) cc_final: 0.5397 (mmp)
REVERT: B 1118 LYS cc_start: 0.7474 (pptt) cc_final: 0.6620 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8287 (OUTLIER) cc_final: 0.8053 (t0)
REVERT: B 1506 GLU cc_start: 0.8285 (pt0) cc_final: 0.8023 (pt0)
REVERT: C  241 CYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8582 (t)
REVERT: D   94 GLU cc_start: 0.7856 (tp30) cc_final: 0.7535 (tp30)
REVERT: D  156 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7472 (t80)
  outliers start: 29
  outliers final: 23
  residues processed: 119
  average time/residue: 0.1036
  time to fit residues: 19.5309
Evaluate side-chains
  117 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1286 LEU
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1500 GLU
Chi-restraints excluded: chain B residue 1562 SER
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 11 optimal weight:    5.9990
   chunk 164 optimal weight:    0.0770
   chunk 20 optimal weight:    4.9990
   chunk 4 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9980
   chunk 167 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 105 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9990
   chunk 113 optimal weight:    2.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.111411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.086245 restraints weight = 28208.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.086582 restraints weight = 22599.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.087408 restraints weight = 19095.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.088133 restraints weight = 15589.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.088270 restraints weight = 14137.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14097  Z= 0.124
  Angle     :  0.592  10.916  19141  Z= 0.304
  Chirality :  0.041   0.163   2162
  Planarity :  0.004   0.050   2434
  Dihedral  :  4.565  22.439   1886
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.65 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.15 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.21), residues: 1761
  helix:  2.53 (0.18), residues: 830
  sheet: -1.09 (0.34), residues: 249
  loop : -2.81 (0.21), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A   6 
 TYR   0.010   0.001   TYR B 935 
 PHE   0.013   0.001   PHE D 150 
 TRP   0.022   0.001   TRP D  47 
 HIS   0.005   0.001   HIS C 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (14097)
  covalent geometry    : angle       0.59191 (19141)
  hydrogen bonds       : bond        0.03514 (  714)
  hydrogen bonds       : angle       3.63778 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 98
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
REVERT: B  773 MET cc_start: 0.8255 (mmm) cc_final: 0.7956 (mmm)
REVERT: B  800 MET cc_start: 0.5918 (tpt) cc_final: 0.5373 (mmp)
REVERT: B 1118 LYS cc_start: 0.7532 (pptt) cc_final: 0.6623 (mmtt)
REVERT: B 1140 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8240 (pp)
REVERT: B 1383 ASP cc_start: 0.8312 (OUTLIER) cc_final: 0.8037 (t0)
REVERT: B 1506 GLU cc_start: 0.8329 (pt0) cc_final: 0.8040 (pt0)
REVERT: C  241 CYS cc_start: 0.9121 (OUTLIER) cc_final: 0.8563 (t)
REVERT: D   94 GLU cc_start: 0.7857 (tp30) cc_final: 0.7534 (tp30)
REVERT: D  156 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.7496 (t80)
  outliers start: 34
  outliers final: 25
  residues processed: 127
  average time/residue: 0.0960
  time to fit residues: 19.6123
Evaluate side-chains
  123 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 94
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1140 LEU
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1286 LEU
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1562 SER
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 42 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 136 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 129 optimal weight:    0.0020
   chunk 169 optimal weight:    0.5980
   chunk 100 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.7590

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

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.110501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.085257 restraints weight = 28318.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.086000 restraints weight = 23010.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.086601 restraints weight = 19172.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.087355 restraints weight = 16471.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.087538 restraints weight = 14851.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14097  Z= 0.140
  Angle     :  0.620  16.740  19141  Z= 0.316
  Chirality :  0.042   0.169   2162
  Planarity :  0.004   0.050   2434
  Dihedral  :  4.620  23.681   1886
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 18.76 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.21), residues: 1761
  helix:  2.52 (0.18), residues: 830
  sheet: -1.16 (0.34), residues: 246
  loop : -2.80 (0.21), residues: 685

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A   6 
 TYR   0.011   0.001   TYR B1536 
 PHE   0.013   0.001   PHE D 150 
 TRP   0.021   0.001   TRP D  47 
 HIS   0.005   0.001   HIS C 126 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (14097)
  covalent geometry    : angle       0.61963 (19141)
  hydrogen bonds       : bond        0.03739 (  714)
  hydrogen bonds       : angle       3.68456 ( 2067)

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

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

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  186 ILE cc_start: 0.8375 (mm) cc_final: 0.7995 (tp)
REVERT: B  773 MET cc_start: 0.8226 (mmm) cc_final: 0.7984 (mmm)
REVERT: B  800 MET cc_start: 0.5848 (tpt) cc_final: 0.5397 (mmp)
REVERT: B 1118 LYS cc_start: 0.7435 (pptt) cc_final: 0.6741 (mmtt)
REVERT: B 1140 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8246 (pp)
REVERT: B 1383 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.8015 (t0)
REVERT: D   94 GLU cc_start: 0.7856 (tp30) cc_final: 0.7354 (tp30)
REVERT: D  156 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7441 (t80)
  outliers start: 30
  outliers final: 27
  residues processed: 119
  average time/residue: 0.0941
  time to fit residues: 18.0518
Evaluate side-chains
  123 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 93
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1140 LEU
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1286 LEU
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1562 SER
Chi-restraints excluded: chain C residue  112 LEU
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  153 SER
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  240 PHE
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 163 optimal weight:    3.9990
   chunk 132 optimal weight:    0.5980
   chunk 171 optimal weight:    1.9990
   chunk 15 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 116 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1089 HIS
** B1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1146 ASN
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1356 ASN ** 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 = 0.3557 r_free = 0.3557 target = 0.106962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.081799 restraints weight = 28501.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.082422 restraints weight = 21997.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.082956 restraints weight = 19347.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.083620 restraints weight = 16025.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.083649 restraints weight = 14618.383|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14097  Z= 0.209
  Angle     :  0.677  16.135  19141  Z= 0.349
  Chirality :  0.044   0.179   2162
  Planarity :  0.004   0.051   2434
  Dihedral  :  4.949  26.146   1886
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.24 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.56 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.21), residues: 1761
  helix:  2.38 (0.18), residues: 832
  sheet: -1.16 (0.34), residues: 238
  loop : -2.90 (0.20), residues: 691

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A   6 
 TYR   0.014   0.002   TYR B1320 
 PHE   0.018   0.002   PHE D 150 
 TRP   0.017   0.002   TRP D  47 
 HIS   0.005   0.001   HIS D 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (14097)
  covalent geometry    : angle       0.67710 (19141)
  hydrogen bonds       : bond        0.04639 (  714)
  hydrogen bonds       : angle       3.94519 ( 2067)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1812.68 seconds
wall clock time: 32 minutes 34.57 seconds (1954.57 seconds total)