Starting phenix.real_space_refine
on Tue Nov 18 19:35:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6e1h_8955/11_2025/6e1h_8955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6e1h_8955/11_2025/6e1h_8955.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6e1h_8955/11_2025/6e1h_8955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6e1h_8955/11_2025/6e1h_8955.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6e1h_8955/11_2025/6e1h_8955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6e1h_8955/11_2025/6e1h_8955.map"
  }
  resolution = 3.5
  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=   0.005 sd=   0.089
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: 6
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      1      6.06       5
     S      90      5.16       5
     C   10834      2.51       5
     N    2762      2.21       5
     O    2978      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16667
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 7667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 978, 7667
          Classifications: {'peptide': 978}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 40, 'TRANS': 937}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "C"
      Number of atoms: 1313
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1313
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 7, 'TRANS': 156}
    Chain: "B"
      Number of atoms: 7667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 978, 7667
          Classifications: {'peptide': 978}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 40, 'TRANS': 937}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 54
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "C"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 20
          Unusual residues: {' CA': 2, ' ZN': 1, 'PLM': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 4.30, per 1000 atoms: 0.26
  Number of scatterers: 16667
  At special positions: 0
  Unit cell: (154, 100, 148, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Ca      2     19.99
     S      90     16.00
     O    2978      8.00
     N    2762      7.00
     C   10834      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 226 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 327 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 203 " - pdb=" SG  CYS B 226 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 234 " - pdb=" SG  CYS B 327 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.46
  Conformation dependent library (CDL) restraints added in 615.6 milliseconds
  

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3968

  Finding SS restraints...
    Secondary structure from input PDB file:
      85 helices and 6 sheets defined
      58.9% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 96
      removed outlier: 4.237A  pdb=" N   ARG A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   LEU A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LYS A  96 " --> pdb=" O   CYS A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 100
    Processing helix  chain 'A' and resid 101 through 117
      removed outlier: 4.307A  pdb=" N   PHE A 112 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 124 through 128
    Processing helix  chain 'A' and resid 134 through 146
      removed outlier: 3.755A  pdb=" N   ARG A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 187
    Processing helix  chain 'A' and resid 215 through 224
    Processing helix  chain 'A' and resid 260 through 271
      removed outlier: 4.146A  pdb=" N   ILE A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 283
      removed outlier: 4.006A  pdb=" N   MET A 281 " --> pdb=" O   SER A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 376
    Processing helix  chain 'A' and resid 388 through 411
      removed outlier: 4.198A  pdb=" N   VAL A 411 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 436
    Processing helix  chain 'A' and resid 438 through 457
      removed outlier: 3.507A  pdb=" N   TYR A 446 " --> pdb=" O   VAL A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 491
    Processing helix  chain 'A' and resid 497 through 502
      removed outlier: 3.766A  pdb=" N   GLN A 501 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 525
      removed outlier: 4.299A  pdb=" N   LEU A 508 " --> pdb=" O   PRO A 504 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   LEU A 517 " --> pdb=" O   ASP A 513 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   LEU A 518 " --> pdb=" O   ASP A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 563
      removed outlier: 5.002A  pdb=" N   ALA A 546 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   SER A 547 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 602
      Proline residue:  A 593  - end of helix
      removed outlier: 3.724A  pdb=" N   MET A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 741
    Processing helix  chain 'A' and resid 742 through 745
      removed outlier: 3.930A  pdb=" N   LEU A 745 " --> pdb=" O   PRO A 742 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 742 through 745'
    Processing helix  chain 'A' and resid 746 through 770
      removed outlier: 3.561A  pdb=" N   LYS A 750 " --> pdb=" O   LYS A 746 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG A 770 " --> pdb=" O   TYR A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 781
      removed outlier: 4.112A  pdb=" N   ILE A 780 " --> pdb=" O   ASP A 776 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL A 781 " --> pdb=" O   LEU A 777 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 776 through 781'
    Processing helix  chain 'A' and resid 785 through 797
      removed outlier: 3.860A  pdb=" N   ASP A 789 " --> pdb=" O   THR A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 825
    Processing helix  chain 'A' and resid 834 through 838
      removed outlier: 3.767A  pdb=" N   ASN A 837 " --> pdb=" O   LEU A 834 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 843 through 866
      removed outlier: 3.537A  pdb=" N   TYR A 847 " --> pdb=" O   MET A 843 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   THR A 865 " --> pdb=" O   SER A 861 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 889
      removed outlier: 3.625A  pdb=" N   VAL A 881 " --> pdb=" O   SER A 877 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLN A 889 " --> pdb=" O   LYS A 885 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 901
    Processing helix  chain 'A' and resid 918 through 930
      removed outlier: 3.807A  pdb=" N   SER A 928 " --> pdb=" O   THR A 924 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 938
    Processing helix  chain 'A' and resid 985 through 1005
    Processing helix  chain 'A' and resid 1012 through 1019
    Processing helix  chain 'A' and resid 1020 through 1022
      No H-bonds generated for 'chain 'A' and resid 1020 through 1022'
    Processing helix  chain 'A' and resid 1023 through 1048
      removed outlier: 3.568A  pdb=" N   TRP A1027 " --> pdb=" O   GLY A1023 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1075
      removed outlier: 3.665A  pdb=" N   GLY A1072 " --> pdb=" O   PHE A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1079 through 1093
      removed outlier: 3.676A  pdb=" N   VAL A1090 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   GLY A1091 " --> pdb=" O   ILE A1087 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1093 through 1104
      removed outlier: 4.159A  pdb=" N   THR A1097 " --> pdb=" O   GLY A1093 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ALA A1103 " --> pdb=" O   HIS A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1122
    Processing helix  chain 'A' and resid 1123 through 1138
    Processing helix  chain 'A' and resid 1139 through 1141
      No H-bonds generated for 'chain 'A' and resid 1139 through 1141'
    Processing helix  chain 'A' and resid 1145 through 1174
      removed outlier: 3.599A  pdb=" N   VAL A1149 " --> pdb=" O   PHE A1145 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   LEU A1171 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      Proline residue:  A1172  - end of helix
    Processing helix  chain 'C' and resid 70 through 76
      removed outlier: 3.847A  pdb=" N   PHE C  73 " --> pdb=" O   SER C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 117
      removed outlier: 3.553A  pdb=" N   SER C 112 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 157 through 169
      removed outlier: 3.729A  pdb=" N   VAL C 166 " --> pdb=" O   ALA C 162 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY C 169 " --> pdb=" O   ALA C 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 95
      removed outlier: 3.985A  pdb=" N   LYS B  82 " --> pdb=" O   TRP B  78 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   PHE B  83 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU B  86 " --> pdb=" O   LYS B  82 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   CYS B  92 " --> pdb=" O   PHE B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 114
    Processing helix  chain 'B' and resid 115 through 118
    Processing helix  chain 'B' and resid 124 through 130
    Processing helix  chain 'B' and resid 135 through 146
      removed outlier: 3.868A  pdb=" N   GLU B 139 " --> pdb=" O   ARG B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 187
      removed outlier: 3.554A  pdb=" N   LEU B 175 " --> pdb=" O   THR B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 222
      removed outlier: 4.020A  pdb=" N   TYR B 222 " --> pdb=" O   GLN B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 271
      removed outlier: 3.793A  pdb=" N   ILE B 271 " --> pdb=" O   GLU B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 285
      removed outlier: 3.671A  pdb=" N   GLU B 280 " --> pdb=" O   ASP B 276 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA B 285 " --> pdb=" O   MET B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 323
      removed outlier: 3.555A  pdb=" N   VAL B 322 " --> pdb=" O   ASP B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 342
      removed outlier: 3.613A  pdb=" N   ILE B 342 " --> pdb=" O   GLN B 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 338 through 342'
    Processing helix  chain 'B' and resid 368 through 376
      removed outlier: 3.789A  pdb=" N   GLU B 374 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 382 through 386
      removed outlier: 4.192A  pdb=" N   ASN B 386 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 409
      removed outlier: 3.540A  pdb=" N   ALA B 392 " --> pdb=" O   ASN B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 436
    Processing helix  chain 'B' and resid 438 through 457
      removed outlier: 3.599A  pdb=" N   GLY B 445 " --> pdb=" O   ARG B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 470 through 491
    Processing helix  chain 'B' and resid 496 through 528
      removed outlier: 4.126A  pdb=" N   THR B 500 " --> pdb=" O   ASN B 496 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   GLN B 501 " --> pdb=" O   ALA B 497 " (cutoff:3.500A)
      Proline residue:  B 504  - end of helix
      removed outlier: 3.823A  pdb=" N   LEU B 518 " --> pdb=" O   ASP B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 561
      removed outlier: 4.234A  pdb=" N   ARG B 543 " --> pdb=" O   GLU B 539 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   SER B 547 " --> pdb=" O   ARG B 543 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   LEU B 550 " --> pdb=" O   ALA B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 567 through 606
      Proline residue:  B 593  - end of helix
      removed outlier: 3.771A  pdb=" N   TYR B 601 " --> pdb=" O   SER B 597 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ARG B 602 " --> pdb=" O   MET B 598 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLU B 604 " --> pdb=" O   LEU B 600 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   ASP B 605 " --> pdb=" O   TYR B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 732 through 744
      removed outlier: 3.748A  pdb=" N   ALA B 736 " --> pdb=" O   LEU B 732 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA B 741 " --> pdb=" O   GLU B 737 " (cutoff:3.500A)
      Proline residue:  B 742  - end of helix
    Processing helix  chain 'B' and resid 746 through 770
      removed outlier: 3.549A  pdb=" N   LYS B 750 " --> pdb=" O   LYS B 746 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TYR B 766 " --> pdb=" O   GLY B 762 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY B 767 " --> pdb=" O   VAL B 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 780
      removed outlier: 4.095A  pdb=" N   ASP B 779 " --> pdb=" O   ASP B 776 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 785 through 797
      removed outlier: 4.291A  pdb=" N   ASP B 789 " --> pdb=" O   THR B 785 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   PHE B 790 " --> pdb=" O   ARG B 786 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ILE B 791 " --> pdb=" O   GLU B 787 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 811 through 814
    Processing helix  chain 'B' and resid 815 through 826
      removed outlier: 3.786A  pdb=" N   TYR B 820 " --> pdb=" O   GLN B 816 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ASP B 821 " --> pdb=" O   HIS B 817 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 834 through 838
      removed outlier: 4.157A  pdb=" N   ASN B 837 " --> pdb=" O   LEU B 834 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 843 through 864
      removed outlier: 3.718A  pdb=" N   TYR B 847 " --> pdb=" O   MET B 843 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 877 through 888
    Processing helix  chain 'B' and resid 915 through 917
      No H-bonds generated for 'chain 'B' and resid 915 through 917'
    Processing helix  chain 'B' and resid 918 through 930
      removed outlier: 4.375A  pdb=" N   ALA B 925 " --> pdb=" O   ILE B 921 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   SER B 928 " --> pdb=" O   THR B 924 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 930 through 937
    Processing helix  chain 'B' and resid 985 through 1004
      removed outlier: 3.535A  pdb=" N   THR B1002 " --> pdb=" O   CYS B 998 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1013 through 1018
    Processing helix  chain 'B' and resid 1023 through 1047
      removed outlier: 4.299A  pdb=" N   SER B1033 " --> pdb=" O   LEU B1029 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1049 through 1075
      removed outlier: 3.610A  pdb=" N   ALA B1053 " --> pdb=" O   ASN B1049 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1079 through 1104
      removed outlier: 3.566A  pdb=" N   VAL B1083 " --> pdb=" O   SER B1079 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   GLY B1091 " --> pdb=" O   ILE B1087 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   VAL B1100 " --> pdb=" O   PHE B1096 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1111 through 1121
      removed outlier: 4.168A  pdb=" N   ALA B1115 " --> pdb=" O   LYS B1111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1122 through 1141
      removed outlier: 3.733A  pdb=" N   VAL B1126 " --> pdb=" O   MET B1122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1145 through 1169
    Processing helix  chain 'B' and resid 1170 through 1175
    Processing sheet with id=AA1, first strand: chain 'A' and resid 153 through 154
    Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344
    Processing sheet with id=AA3, first strand: chain 'A' and resid 972 through 979
      removed outlier: 3.800A  pdb=" N   ASN A1011 " --> pdb=" O   TYR A 804 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 84 through 86
      removed outlier: 6.505A  pdb=" N   ILE C  85 " --> pdb=" O   VAL C 124 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 343 through 344
    Processing sheet with id=AA6, first strand: chain 'B' and resid 972 through 979
      removed outlier: 3.530A  pdb=" N   ILE B 805 " --> pdb=" O   PHE B 974 " (cutoff:3.500A)

    877 hydrogen bonds defined for protein.
    2559 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: 2.95

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2903
        1.32 -     1.45: 4542
        1.45 -     1.57: 9476
        1.57 -     1.70: 1
        1.70 -     1.82: 147
  Bond restraints: 17069
  Sorted by residual:
  bond pdb=" N   LEU B1048 "
       pdb=" CA  LEU B1048 "
    ideal  model  delta    sigma   weight residual
    1.457  1.513 -0.056 1.29e-02 6.01e+03 1.88e+01
  bond pdb=" N   CYS C  24 "
       pdb=" CA  CYS C  24 "
    ideal  model  delta    sigma   weight residual
    1.458  1.532 -0.074 1.90e-02 2.77e+03 1.51e+01
  bond pdb=" CA  PLM C 204 "
       pdb=" CB  PLM C 204 "
    ideal  model  delta    sigma   weight residual
    1.524  1.600 -0.076 2.00e-02 2.50e+03 1.46e+01
  bond pdb=" N   LEU A 297 "
       pdb=" CA  LEU A 297 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.039 1.15e-02 7.56e+03 1.13e+01
  bond pdb=" C   CYS B 304 "
       pdb=" N   PRO B 305 "
    ideal  model  delta    sigma   weight residual
    1.334  1.362 -0.028 8.40e-03 1.42e+04 1.11e+01
  ... (remaining 17064 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 21961
        2.28 -     4.57: 1153
        4.57 -     6.85: 70
        6.85 -     9.14: 9
        9.14 -    11.42: 3
  Bond angle restraints: 23196
  Sorted by residual:
  angle pdb=" N   PRO A 896 "
        pdb=" CA  PRO A 896 "
        pdb=" CB  PRO A 896 "
      ideal   model   delta    sigma   weight residual
     103.25  110.79   -7.54 1.05e+00 9.07e-01 5.16e+01
  angle pdb=" N   PRO B 896 "
        pdb=" CA  PRO B 896 "
        pdb=" CB  PRO B 896 "
      ideal   model   delta    sigma   weight residual
     103.25  110.52   -7.27 1.05e+00 9.07e-01 4.80e+01
  angle pdb=" N   PRO A 225 "
        pdb=" CA  PRO A 225 "
        pdb=" C   PRO A 225 "
      ideal   model   delta    sigma   weight residual
     112.47  123.89  -11.42 2.06e+00 2.36e-01 3.07e+01
  angle pdb=" C   PHE A 101 "
        pdb=" N   LEU A 102 "
        pdb=" CA  LEU A 102 "
      ideal   model   delta    sigma   weight residual
     120.44  126.73   -6.29 1.30e+00 5.92e-01 2.34e+01
  angle pdb=" N   PRO B 225 "
        pdb=" CA  PRO B 225 "
        pdb=" C   PRO B 225 "
      ideal   model   delta    sigma   weight residual
     113.84  119.99   -6.15 1.30e+00 5.92e-01 2.24e+01
  ... (remaining 23191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 9273
       16.82 -    33.65: 665
       33.65 -    50.47: 125
       50.47 -    67.29: 11
       67.29 -    84.11: 9
  Dihedral angle restraints: 10083
    sinusoidal: 3909
      harmonic: 6174
  Sorted by residual:
  dihedral pdb=" CB  CYS A 203 "
           pdb=" SG  CYS A 203 "
           pdb=" SG  CYS A 226 "
           pdb=" CB  CYS A 226 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.07   68.07     1      1.00e+01 1.00e-02 6.01e+01
  dihedral pdb=" CA  TRP A 197 "
           pdb=" C   TRP A 197 "
           pdb=" N   LYS A 198 "
           pdb=" CA  LYS A 198 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.31  -35.69     0      5.00e+00 4.00e-02 5.10e+01
  dihedral pdb=" CA  TRP B 197 "
           pdb=" C   TRP B 197 "
           pdb=" N   LYS B 198 "
           pdb=" CA  LYS B 198 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.84  -33.16     0      5.00e+00 4.00e-02 4.40e+01
  ... (remaining 10080 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1743
       0.059 -    0.118: 711
       0.118 -    0.177: 159
       0.177 -    0.236: 15
       0.236 -    0.295: 4
  Chirality restraints: 2632
  Sorted by residual:
  chirality pdb=" CA  PRO A 225 "
            pdb=" N   PRO A 225 "
            pdb=" C   PRO A 225 "
            pdb=" CB  PRO A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.42    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CB  ILE B 210 "
            pdb=" CA  ILE B 210 "
            pdb=" CG1 ILE B 210 "
            pdb=" CG2 ILE B 210 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  ASN B 584 "
            pdb=" N   ASN B 584 "
            pdb=" C   ASN B 584 "
            pdb=" CB  ASN B 584 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 2629 not shown)

  Planarity restraints: 2921
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 894 "    0.015 2.00e-02 2.50e+03   3.06e-02 9.37e+00
        pdb=" C   ASP B 894 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ASP B 894 "    0.020 2.00e-02 2.50e+03
        pdb=" N   LYS B 895 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 197 "   -0.029 2.00e-02 2.50e+03   1.82e-02 8.30e+00
        pdb=" CG  TRP A 197 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 197 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 197 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 197 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 197 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 197 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 197 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 197 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 197 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 197 "   -0.027 2.00e-02 2.50e+03   1.70e-02 7.20e+00
        pdb=" CG  TRP B 197 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 197 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 197 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 197 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 197 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 197 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 197 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 197 "    0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 197 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2918 not shown)

  Histogram of nonbonded interaction distances:
        1.96 -     2.55: 69
        2.55 -     3.14: 12388
        3.14 -     3.72: 26642
        3.72 -     4.31: 36161
        4.31 -     4.90: 59123
  Nonbonded interactions: 134383
  Sorted by model distance:
  nonbonded pdb=" O   THR C 125 "
            pdb="CA    CA C 202 "
     model   vdw
     1.962 2.510
  nonbonded pdb=" O   SER C 135 "
            pdb=" OH  TYR C 141 "
     model   vdw
     2.272 3.040
  nonbonded pdb="CA    CA C 202 "
            pdb="CA    CA C 203 "
     model   vdw
     2.272 1.980
  nonbonded pdb=" O   PRO B 309 "
            pdb=" N   SER B 313 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   TYR A 766 "
            pdb=" OG1 THR A 769 "
     model   vdw
     2.315 3.040
  ... (remaining 134378 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 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     16.380
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7519
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      :  0.008   0.108  17074  Z= 0.540
  Angle     :  1.177  11.420  23204  Z= 0.775
  Chirality :  0.064   0.295   2632
  Planarity :  0.005   0.041   2921
  Dihedral  : 12.247  84.113   6103
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.86 %
    Favored  : 90.09 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  6.26 %
    Favored  : 91.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.67 (0.15), residues: 2110
  helix: -1.73 (0.13), residues: 1150
  sheet: -3.11 (0.40), residues: 111
  loop : -3.26 (0.18), residues: 849

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 536 
 TYR   0.034   0.003   TYR A 224 
 PHE   0.026   0.002   PHE B 790 
 TRP   0.049   0.003   TRP A 197 
 HIS   0.007   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00777 (17069)
  covalent geometry    : angle       1.17575 (23196)
  SS BOND              : bond        0.00575 (    4)
  SS BOND              : angle       2.54871 (    8)
  hydrogen bonds       : bond        0.13502 (  877)
  hydrogen bonds       : angle       7.32379 ( 2559)
  Misc. bond           : bond        0.10764 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  696 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 665
  time to evaluate  : 0.659 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 GLN cc_start: 0.8701 (pt0) cc_final: 0.7982 (pt0)
REVERT: A  156 GLN cc_start: 0.8508 (mp10) cc_final: 0.8246 (mp10)
REVERT: A  157 LEU cc_start: 0.8967 (mp) cc_final: 0.8567 (mt)
REVERT: A  373 TYR cc_start: 0.8180 (t80) cc_final: 0.7902 (t80)
REVERT: A  428 ASP cc_start: 0.8281 (t70) cc_final: 0.7736 (t0)
REVERT: A  567 ILE cc_start: 0.8192 (mp) cc_final: 0.7670 (mt)
REVERT: A  922 TYR cc_start: 0.7926 (m-80) cc_final: 0.7417 (m-80)
REVERT: A 1028 LEU cc_start: 0.8954 (tp) cc_final: 0.8738 (tp)
REVERT: A 1048 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5382 (tp)
REVERT: A 1051 TRP cc_start: 0.4879 (t60) cc_final: 0.4602 (t60)
REVERT: A 1063 MET cc_start: 0.8481 (mtp) cc_final: 0.8168 (mtp)
REVERT: A 1162 LEU cc_start: 0.9140 (mt) cc_final: 0.8934 (mm)
REVERT: A 1166 ASN cc_start: 0.7898 (m110) cc_final: 0.7465 (m110)
REVERT: C  114 MET cc_start: 0.8132 (mtm) cc_final: 0.7791 (mtm)
REVERT: B  153 PHE cc_start: 0.8108 (p90) cc_final: 0.6997 (p90)
REVERT: B  158 MET cc_start: 0.7695 (ttp) cc_final: 0.7463 (ttp)
REVERT: B  221 GLU cc_start: 0.7959 (tt0) cc_final: 0.7086 (tt0)
REVERT: B  222 TYR cc_start: 0.7550 (m-80) cc_final: 0.7150 (m-10)
REVERT: B  424 THR cc_start: 0.8698 (p) cc_final: 0.8491 (t)
REVERT: B  432 LYS cc_start: 0.8878 (mttm) cc_final: 0.8449 (mmtt)
REVERT: B  479 LEU cc_start: 0.7242 (OUTLIER) cc_final: 0.6951 (mm)
REVERT: B  835 GLU cc_start: 0.6978 (pp20) cc_final: 0.6753 (pp20)
REVERT: B  882 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8393 (tm)
REVERT: B  922 TYR cc_start: 0.8726 (m-10) cc_final: 0.8136 (m-80)
REVERT: B 1028 LEU cc_start: 0.9088 (tp) cc_final: 0.8856 (tp)
REVERT: B 1063 MET cc_start: 0.8688 (mtp) cc_final: 0.8325 (mtt)
REVERT: B 1121 HIS cc_start: 0.7122 (p-80) cc_final: 0.6707 (p-80)
  outliers start: 31
  outliers final: 7
  residues processed: 683
  average time/residue: 0.1382
  time to fit residues: 139.7073
Evaluate side-chains
  442 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 432
  time to evaluate  : 0.670 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  541 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue  807 THR
Chi-restraints excluded: chain B residue  882 LEU
Chi-restraints excluded: chain B residue 1135 LEU
Chi-restraints excluded: chain B residue 1169 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 194 optimal weight:    1.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 200 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 124 ASN
A 310 ASN
A 324 ASN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 ASN
A 794 GLN
A 837 ASN
A 929 ASN
A 940 ASN
A1099 HIS
C 140 HIS
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 189 HIS
** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
B 310 ASN
B 324 ASN
B 358 HIS
B 375 HIS
** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 576 GLN
B 584 ASN
B 837 ASN
B 872 ASN
B 889 GLN
B 929 ASN
B1166 ASN

Total number of N/Q/H flips: 23

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.122704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.104941 restraints weight = 39840.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.107854 restraints weight = 19292.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.109710 restraints weight = 11675.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.110979 restraints weight = 8251.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.111714 restraints weight = 6465.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  17074  Z= 0.173
  Angle     :  0.779  12.934  23204  Z= 0.389
  Chirality :  0.045   0.303   2632
  Planarity :  0.005   0.064   2921
  Dihedral  :  7.165  57.521   2323
  Min Nonbonded Distance : 1.717

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 15.98 %
    Favored  : 79.35 %
  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: -2.13 (0.17), residues: 2110
  helix: -0.36 (0.14), residues: 1166
  sheet: -2.76 (0.40), residues: 114
  loop : -2.74 (0.20), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 772 
 TYR   0.026   0.002   TYR C  62 
 PHE   0.057   0.002   PHE B 790 
 TRP   0.021   0.002   TRP A 197 
 HIS   0.008   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (17069)
  covalent geometry    : angle       0.77864 (23196)
  SS BOND              : bond        0.00312 (    4)
  SS BOND              : angle       0.63919 (    8)
  hydrogen bonds       : bond        0.04641 (  877)
  hydrogen bonds       : angle       5.20970 ( 2559)
  Misc. bond           : bond        0.00031 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  538 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 456
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 LEU cc_start: 0.8836 (mp) cc_final: 0.8585 (mt)
REVERT: A  194 ASN cc_start: 0.7837 (m-40) cc_final: 0.7510 (t0)
REVERT: A  363 MET cc_start: 0.8700 (mtp) cc_final: 0.8301 (mtp)
REVERT: A  428 ASP cc_start: 0.8560 (t70) cc_final: 0.7883 (t0)
REVERT: A  598 MET cc_start: 0.7824 (mpp) cc_final: 0.7424 (mmt)
REVERT: A  886 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8317 (mm)
REVERT: A  922 TYR cc_start: 0.8472 (m-80) cc_final: 0.7781 (m-80)
REVERT: A 1047 LEU cc_start: 0.8085 (mp) cc_final: 0.7811 (mt)
REVERT: A 1048 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.5391 (tp)
REVERT: A 1049 ASN cc_start: 0.8241 (m-40) cc_final: 0.7788 (m110)
REVERT: A 1162 LEU cc_start: 0.9248 (mt) cc_final: 0.9009 (mm)
REVERT: A 1166 ASN cc_start: 0.7823 (m110) cc_final: 0.7298 (m110)
REVERT: B  221 GLU cc_start: 0.8348 (tt0) cc_final: 0.7504 (tt0)
REVERT: B  222 TYR cc_start: 0.7947 (m-80) cc_final: 0.7388 (m-10)
REVERT: B  249 LEU cc_start: 0.6823 (mm) cc_final: 0.6238 (mt)
REVERT: B  332 ARG cc_start: 0.4660 (mpt-90) cc_final: 0.1660 (mpt-90)
REVERT: B  377 LYS cc_start: 0.8975 (ttmm) cc_final: 0.8658 (ttmm)
REVERT: B  432 LYS cc_start: 0.8605 (mttm) cc_final: 0.8058 (mmmt)
REVERT: B  464 LYS cc_start: 0.7137 (mttt) cc_final: 0.6787 (mttp)
REVERT: B  479 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6777 (tp)
REVERT: B  534 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7631 (mp0)
REVERT: B  597 SER cc_start: 0.8467 (p) cc_final: 0.8260 (m)
REVERT: B  776 ASP cc_start: 0.7341 (p0) cc_final: 0.7081 (p0)
REVERT: B  788 TYR cc_start: 0.7754 (t80) cc_final: 0.7352 (t80)
REVERT: B  886 LEU cc_start: 0.9299 (mt) cc_final: 0.9068 (mp)
REVERT: B  922 TYR cc_start: 0.9088 (m-10) cc_final: 0.8158 (m-80)
REVERT: B  929 ASN cc_start: 0.8630 (m-40) cc_final: 0.8193 (m110)
REVERT: B  932 VAL cc_start: 0.9080 (t) cc_final: 0.7678 (p)
REVERT: B 1052 THR cc_start: 0.9396 (m) cc_final: 0.9136 (p)
REVERT: B 1139 MET cc_start: 0.8754 (tmm) cc_final: 0.8439 (tmm)
REVERT: B 1153 PHE cc_start: 0.8943 (t80) cc_final: 0.8742 (t80)
  outliers start: 82
  outliers final: 40
  residues processed: 505
  average time/residue: 0.1155
  time to fit residues: 92.3731
Evaluate side-chains
  428 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 385
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1143 SER
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  323 LEU
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  436 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  541 LEU
Chi-restraints excluded: chain B residue  739 HIS
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue  837 ASN
Chi-restraints excluded: chain B residue  879 ASP
Chi-restraints excluded: chain B residue  998 CYS
Chi-restraints excluded: chain B residue 1029 LEU
Chi-restraints excluded: chain B residue 1039 THR
Chi-restraints excluded: chain B residue 1064 THR
Chi-restraints excluded: chain B residue 1100 VAL
Chi-restraints excluded: chain B residue 1128 ASP
Chi-restraints excluded: chain B residue 1140 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 171 optimal weight:    0.8980
   chunk 76 optimal weight:    1.9990
   chunk 33 optimal weight:    8.9990
   chunk 52 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 102 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 197 optimal weight:    3.9990
   chunk 108 optimal weight:    7.9990
   chunk 162 optimal weight:    0.6980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 739 HIS
A 839 GLN
A1099 HIS
C 115 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 178 HIS
B 258 ASN
B 324 ASN
** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 ASN
B 940 ASN
B1166 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.120356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.102537 restraints weight = 40291.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.105459 restraints weight = 19352.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.107264 restraints weight = 11674.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.108544 restraints weight = 8288.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.109264 restraints weight = 6496.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  17074  Z= 0.186
  Angle     :  0.742  11.943  23204  Z= 0.371
  Chirality :  0.045   0.329   2632
  Planarity :  0.005   0.066   2921
  Dihedral  :  6.633  59.151   2313
  Min Nonbonded Distance : 1.753

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 18.43 %
    Favored  : 76.11 %
  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: -1.51 (0.18), residues: 2110
  helix:  0.15 (0.15), residues: 1174
  sheet: -2.47 (0.43), residues: 117
  loop : -2.49 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1113 
 TYR   0.026   0.002   TYR A 740 
 PHE   0.041   0.002   PHE B 790 
 TRP   0.019   0.001   TRP A 197 
 HIS   0.006   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (17069)
  covalent geometry    : angle       0.74184 (23196)
  SS BOND              : bond        0.00849 (    4)
  SS BOND              : angle       0.92596 (    8)
  hydrogen bonds       : bond        0.04353 (  877)
  hydrogen bonds       : angle       4.99109 ( 2559)
  Misc. bond           : bond        0.00073 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  505 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 409
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 LEU cc_start: 0.8888 (mp) cc_final: 0.8620 (mt)
REVERT: A  194 ASN cc_start: 0.7795 (m-40) cc_final: 0.7516 (t0)
REVERT: A  216 MET cc_start: 0.8009 (mmm) cc_final: 0.7755 (mmm)
REVERT: A  363 MET cc_start: 0.8693 (mtp) cc_final: 0.8358 (mtm)
REVERT: A  428 ASP cc_start: 0.8598 (t70) cc_final: 0.7923 (t0)
REVERT: A  598 MET cc_start: 0.7676 (mpp) cc_final: 0.7308 (mmt)
REVERT: A  602 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7113 (mmt180)
REVERT: A  740 TYR cc_start: 0.4827 (m-80) cc_final: 0.4487 (m-80)
REVERT: A  760 LEU cc_start: 0.8594 (tt) cc_final: 0.8308 (tt)
REVERT: A  886 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8302 (mm)
REVERT: A  922 TYR cc_start: 0.8471 (m-80) cc_final: 0.7937 (m-80)
REVERT: A 1048 LEU cc_start: 0.5645 (OUTLIER) cc_final: 0.5076 (tt)
REVERT: A 1049 ASN cc_start: 0.8156 (m-40) cc_final: 0.7591 (m-40)
REVERT: A 1122 MET cc_start: 0.8671 (mtt) cc_final: 0.8411 (mtp)
REVERT: B   93 TYR cc_start: 0.5737 (OUTLIER) cc_final: 0.4998 (t80)
REVERT: B  127 GLU cc_start: 0.8025 (tp30) cc_final: 0.7807 (tp30)
REVERT: B  153 PHE cc_start: 0.8586 (p90) cc_final: 0.8337 (p90)
REVERT: B  216 MET cc_start: 0.8805 (mmm) cc_final: 0.8527 (tpt)
REVERT: B  221 GLU cc_start: 0.8267 (tt0) cc_final: 0.7469 (tt0)
REVERT: B  222 TYR cc_start: 0.7973 (m-80) cc_final: 0.7435 (m-10)
REVERT: B  330 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6953 (mp)
REVERT: B  332 ARG cc_start: 0.4723 (mpt-90) cc_final: 0.1611 (mpt-90)
REVERT: B  370 LYS cc_start: 0.8602 (mppt) cc_final: 0.8366 (tptp)
REVERT: B  377 LYS cc_start: 0.9002 (ttmm) cc_final: 0.8620 (ttmm)
REVERT: B  432 LYS cc_start: 0.8682 (mttm) cc_final: 0.8137 (mmmt)
REVERT: B  464 LYS cc_start: 0.7226 (mttt) cc_final: 0.6871 (mttp)
REVERT: B  536 ARG cc_start: 0.6655 (ttt90) cc_final: 0.6303 (tpt-90)
REVERT: B  776 ASP cc_start: 0.7402 (p0) cc_final: 0.7128 (p0)
REVERT: B  788 TYR cc_start: 0.7823 (t80) cc_final: 0.7470 (t80)
REVERT: B  922 TYR cc_start: 0.9083 (m-10) cc_final: 0.8219 (m-80)
REVERT: B 1058 MET cc_start: 0.8741 (mtm) cc_final: 0.8463 (mtt)
REVERT: B 1066 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7941 (mt-10)
REVERT: B 1139 MET cc_start: 0.8814 (tmm) cc_final: 0.8344 (tmm)
REVERT: B 1153 PHE cc_start: 0.8935 (t80) cc_final: 0.8694 (t80)
  outliers start: 96
  outliers final: 55
  residues processed: 464
  average time/residue: 0.1146
  time to fit residues: 85.6771
Evaluate side-chains
  423 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 364
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1143 SER
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  324 ASN
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  436 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  739 HIS
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  806 VAL
Chi-restraints excluded: chain B residue  879 ASP
Chi-restraints excluded: chain B residue  998 CYS
Chi-restraints excluded: chain B residue 1029 LEU
Chi-restraints excluded: chain B residue 1039 THR
Chi-restraints excluded: chain B residue 1100 VAL
Chi-restraints excluded: chain B residue 1128 ASP
Chi-restraints excluded: chain B residue 1140 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 189 optimal weight:    9.9990
   chunk 155 optimal weight:    2.9990
   chunk 153 optimal weight:    2.9990
   chunk 209 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 115 optimal weight:    6.9990
   chunk 17 optimal weight:    3.9990
   chunk 152 optimal weight:    8.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
A 310 ASN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 527 GLN
A1020 GLN
C 115 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 ASN
** B 384 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 837 ASN
B1099 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.117586 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.100228 restraints weight = 40015.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.103041 restraints weight = 19132.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.104830 restraints weight = 11537.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.105885 restraints weight = 8160.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.106670 restraints weight = 6526.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.4146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  17074  Z= 0.221
  Angle     :  0.751  11.277  23204  Z= 0.378
  Chirality :  0.046   0.275   2632
  Planarity :  0.005   0.054   2921
  Dihedral  :  6.382  58.818   2311
  Min Nonbonded Distance : 1.765

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.44 %
    Favored  : 91.56 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 20.19 %
    Favored  : 73.83 %
  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: -1.24 (0.18), residues: 2110
  helix:  0.40 (0.15), residues: 1179
  sheet: -2.23 (0.45), residues: 117
  loop : -2.45 (0.21), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 332 
 TYR   0.020   0.002   TYR A 873 
 PHE   0.035   0.002   PHE B 790 
 TRP   0.022   0.002   TRP A 197 
 HIS   0.007   0.001   HIS B 950 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 (17069)
  covalent geometry    : angle       0.75145 (23196)
  SS BOND              : bond        0.00582 (    4)
  SS BOND              : angle       0.59920 (    8)
  hydrogen bonds       : bond        0.04302 (  877)
  hydrogen bonds       : angle       4.90556 ( 2559)
  Misc. bond           : bond        0.00070 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  494 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 105
    poor density    : 389
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.8446 (t0) cc_final: 0.8229 (t0)
REVERT: A  131 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6749 (mp0)
REVERT: A  194 ASN cc_start: 0.7874 (m-40) cc_final: 0.7672 (t0)
REVERT: A  363 MET cc_start: 0.8703 (mtp) cc_final: 0.8414 (mtm)
REVERT: A  428 ASP cc_start: 0.8661 (t70) cc_final: 0.7981 (t0)
REVERT: A  501 GLN cc_start: 0.7952 (mt0) cc_final: 0.7493 (mt0)
REVERT: A  598 MET cc_start: 0.7658 (mpp) cc_final: 0.7275 (mmt)
REVERT: A  602 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7151 (mmt180)
REVERT: A  740 TYR cc_start: 0.5052 (m-80) cc_final: 0.4772 (m-80)
REVERT: A  886 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8452 (mm)
REVERT: A  889 GLN cc_start: 0.8228 (tt0) cc_final: 0.7887 (tt0)
REVERT: A  977 TYR cc_start: 0.8343 (m-10) cc_final: 0.8141 (m-80)
REVERT: A 1048 LEU cc_start: 0.5549 (OUTLIER) cc_final: 0.5246 (tp)
REVERT: A 1049 ASN cc_start: 0.8109 (m-40) cc_final: 0.7619 (m-40)
REVERT: A 1066 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8376 (mt-10)
REVERT: A 1122 MET cc_start: 0.8661 (mtt) cc_final: 0.8378 (mtp)
REVERT: C   98 MET cc_start: 0.8630 (mtp) cc_final: 0.8264 (mtp)
REVERT: B   93 TYR cc_start: 0.5724 (OUTLIER) cc_final: 0.5091 (t80)
REVERT: B  127 GLU cc_start: 0.8140 (tp30) cc_final: 0.7865 (tp30)
REVERT: B  221 GLU cc_start: 0.8220 (tt0) cc_final: 0.7358 (tt0)
REVERT: B  222 TYR cc_start: 0.7942 (m-80) cc_final: 0.7439 (m-10)
REVERT: B  330 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7186 (mp)
REVERT: B  332 ARG cc_start: 0.4669 (mpt-90) cc_final: 0.1502 (mpt-90)
REVERT: B  370 LYS cc_start: 0.8621 (mppt) cc_final: 0.8353 (tptp)
REVERT: B  432 LYS cc_start: 0.8708 (mttm) cc_final: 0.8182 (mmtt)
REVERT: B  496 ASN cc_start: 0.8850 (t0) cc_final: 0.8501 (t0)
REVERT: B  501 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.6961 (mp10)
REVERT: B  536 ARG cc_start: 0.6547 (ttt90) cc_final: 0.6243 (tpt-90)
REVERT: B  776 ASP cc_start: 0.7556 (p0) cc_final: 0.7245 (p0)
REVERT: B  788 TYR cc_start: 0.7988 (t80) cc_final: 0.7663 (t80)
REVERT: B  922 TYR cc_start: 0.9108 (m-10) cc_final: 0.8227 (m-80)
REVERT: B 1040 PHE cc_start: 0.7689 (t80) cc_final: 0.7430 (t80)
REVERT: B 1058 MET cc_start: 0.8662 (mtm) cc_final: 0.8414 (mtt)
REVERT: B 1066 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8088 (mt-10)
REVERT: B 1139 MET cc_start: 0.8786 (tmm) cc_final: 0.8389 (tmm)
REVERT: B 1153 PHE cc_start: 0.8914 (t80) cc_final: 0.8655 (t80)
  outliers start: 105
  outliers final: 62
  residues processed: 449
  average time/residue: 0.1094
  time to fit residues: 78.8223
Evaluate side-chains
  424 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 356
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1100 VAL
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1143 SER
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  340 GLU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  436 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  479 LEU
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  501 GLN
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  739 HIS
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  837 ASN
Chi-restraints excluded: chain B residue  879 ASP
Chi-restraints excluded: chain B residue  998 CYS
Chi-restraints excluded: chain B residue 1029 LEU
Chi-restraints excluded: chain B residue 1039 THR
Chi-restraints excluded: chain B residue 1064 THR
Chi-restraints excluded: chain B residue 1100 VAL
Chi-restraints excluded: chain B residue 1128 ASP
Chi-restraints excluded: chain B residue 1148 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 124 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 149 optimal weight:    4.9990
   chunk 168 optimal weight:    5.9990
   chunk 194 optimal weight:    3.9990
   chunk 173 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 103 optimal weight:    7.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 258 ASN
A 310 ASN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 168 ASN
B 324 ASN
B 358 HIS
** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1099 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.118819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.101749 restraints weight = 39817.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.104553 restraints weight = 18755.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.106259 restraints weight = 11256.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.107405 restraints weight = 8017.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.108155 restraints weight = 6362.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.4355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  17074  Z= 0.170
  Angle     :  0.736  10.544  23204  Z= 0.363
  Chirality :  0.045   0.236   2632
  Planarity :  0.005   0.051   2921
  Dihedral  :  6.191  58.414   2310
  Min Nonbonded Distance : 1.775

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 21.50 %
    Favored  : 73.49 %
  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: -1.05 (0.18), residues: 2110
  helix:  0.49 (0.15), residues: 1182
  sheet: -1.98 (0.47), residues: 114
  loop : -2.30 (0.21), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 770 
 TYR   0.019   0.002   TYR A 873 
 PHE   0.028   0.002   PHE B 790 
 TRP   0.020   0.001   TRP A 197 
 HIS   0.006   0.001   HIS B1121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (17069)
  covalent geometry    : angle       0.73578 (23196)
  SS BOND              : bond        0.00377 (    4)
  SS BOND              : angle       0.75864 (    8)
  hydrogen bonds       : bond        0.04139 (  877)
  hydrogen bonds       : angle       4.82147 ( 2559)
  Misc. bond           : bond        0.00063 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  484 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 396
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.8418 (t0) cc_final: 0.8169 (t0)
REVERT: A  131 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.6591 (mp0)
REVERT: A  216 MET cc_start: 0.7987 (mmm) cc_final: 0.7737 (mmm)
REVERT: A  363 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8341 (mtm)
REVERT: A  501 GLN cc_start: 0.7925 (mt0) cc_final: 0.7479 (mt0)
REVERT: A  587 MET cc_start: 0.8222 (tmm) cc_final: 0.7914 (tmm)
REVERT: A  598 MET cc_start: 0.7632 (mpp) cc_final: 0.7291 (mmt)
REVERT: A  602 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7116 (mmt180)
REVERT: A  886 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8441 (mm)
REVERT: A  977 TYR cc_start: 0.8308 (m-10) cc_final: 0.8104 (m-80)
REVERT: A 1048 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.5260 (tp)
REVERT: A 1049 ASN cc_start: 0.8193 (m-40) cc_final: 0.7804 (m-40)
REVERT: A 1066 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8211 (mt-10)
REVERT: A 1070 MET cc_start: 0.8561 (mmm) cc_final: 0.8108 (mmm)
REVERT: A 1122 MET cc_start: 0.8651 (mtt) cc_final: 0.8396 (mtt)
REVERT: B   93 TYR cc_start: 0.5733 (OUTLIER) cc_final: 0.5110 (t80)
REVERT: B  127 GLU cc_start: 0.8135 (tp30) cc_final: 0.7840 (tp30)
REVERT: B  221 GLU cc_start: 0.8182 (tt0) cc_final: 0.7510 (tt0)
REVERT: B  222 TYR cc_start: 0.7945 (m-80) cc_final: 0.7530 (m-10)
REVERT: B  330 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7106 (mp)
REVERT: B  332 ARG cc_start: 0.4646 (mpt-90) cc_final: 0.1486 (mpt-90)
REVERT: B  370 LYS cc_start: 0.8603 (mppt) cc_final: 0.8297 (tptp)
REVERT: B  432 LYS cc_start: 0.8719 (mttm) cc_final: 0.8207 (mmtt)
REVERT: B  496 ASN cc_start: 0.8829 (t0) cc_final: 0.8434 (t0)
REVERT: B  536 ARG cc_start: 0.6433 (ttt90) cc_final: 0.6155 (tpt-90)
REVERT: B  776 ASP cc_start: 0.7560 (p0) cc_final: 0.7244 (p0)
REVERT: B  788 TYR cc_start: 0.7959 (t80) cc_final: 0.7666 (t80)
REVERT: B  922 TYR cc_start: 0.9116 (m-10) cc_final: 0.8252 (m-80)
REVERT: B 1040 PHE cc_start: 0.7675 (t80) cc_final: 0.7336 (t80)
REVERT: B 1058 MET cc_start: 0.8610 (mtm) cc_final: 0.8405 (mtt)
REVERT: B 1099 HIS cc_start: 0.8678 (m170) cc_final: 0.8291 (m-70)
REVERT: B 1139 MET cc_start: 0.8745 (tmm) cc_final: 0.8539 (tmm)
REVERT: B 1153 PHE cc_start: 0.8878 (t80) cc_final: 0.8625 (t80)
  outliers start: 88
  outliers final: 60
  residues processed: 445
  average time/residue: 0.1121
  time to fit residues: 80.0111
Evaluate side-chains
  432 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 366
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  172 THR
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  363 MET
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1100 VAL
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1143 SER
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  212 GLU
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  324 ASN
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  436 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  564 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  739 HIS
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  879 ASP
Chi-restraints excluded: chain B residue  998 CYS
Chi-restraints excluded: chain B residue 1029 LEU
Chi-restraints excluded: chain B residue 1039 THR
Chi-restraints excluded: chain B residue 1064 THR
Chi-restraints excluded: chain B residue 1128 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 172 optimal weight:    8.9990
   chunk 137 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 66 optimal weight:    5.9990
   chunk 84 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 157 optimal weight:    6.9990
   chunk 102 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 69 optimal weight:    9.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 324 ASN
B 358 HIS
** B 417 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 = 0.3747 r_free = 0.3747 target = 0.121321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.104356 restraints weight = 39612.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.107096 restraints weight = 18370.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.108867 restraints weight = 11109.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.109901 restraints weight = 7883.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.110720 restraints weight = 6315.899|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.4599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  17074  Z= 0.160
  Angle     :  0.720  10.594  23204  Z= 0.357
  Chirality :  0.044   0.241   2632
  Planarity :  0.005   0.049   2921
  Dihedral  :  6.033  57.190   2310
  Min Nonbonded Distance : 1.792

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 21.16 %
    Favored  : 73.09 %
  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: -0.84 (0.18), residues: 2110
  helix:  0.66 (0.15), residues: 1175
  sheet: -1.93 (0.47), residues: 116
  loop : -2.19 (0.21), residues: 819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 155 
 TYR   0.019   0.002   TYR A 873 
 PHE   0.027   0.001   PHE B 790 
 TRP   0.019   0.001   TRP A 197 
 HIS   0.005   0.001   HIS A 950 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 (17069)
  covalent geometry    : angle       0.72044 (23196)
  SS BOND              : bond        0.00384 (    4)
  SS BOND              : angle       0.59040 (    8)
  hydrogen bonds       : bond        0.04003 (  877)
  hydrogen bonds       : angle       4.76557 ( 2559)
  Misc. bond           : bond        0.00033 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  499 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 398
  time to evaluate  : 0.597 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.6515 (mp0)
REVERT: A  157 LEU cc_start: 0.8968 (mp) cc_final: 0.8596 (mt)
REVERT: A  216 MET cc_start: 0.8006 (mmm) cc_final: 0.7678 (mmm)
REVERT: A  282 LEU cc_start: 0.8830 (mt) cc_final: 0.8547 (mt)
REVERT: A  501 GLN cc_start: 0.7971 (mt0) cc_final: 0.7359 (mt0)
REVERT: A  598 MET cc_start: 0.7659 (mpp) cc_final: 0.7318 (mmt)
REVERT: A  602 ARG cc_start: 0.7670 (mtt-85) cc_final: 0.7051 (mmt180)
REVERT: A  886 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8458 (mm)
REVERT: A  977 TYR cc_start: 0.8313 (m-10) cc_final: 0.8075 (m-80)
REVERT: A 1049 ASN cc_start: 0.8244 (m-40) cc_final: 0.7850 (m-40)
REVERT: A 1066 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8225 (mt-10)
REVERT: A 1094 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8287 (t)
REVERT: A 1122 MET cc_start: 0.8628 (mtt) cc_final: 0.8393 (mtt)
REVERT: B   93 TYR cc_start: 0.5769 (OUTLIER) cc_final: 0.5042 (t80)
REVERT: B  127 GLU cc_start: 0.8224 (tp30) cc_final: 0.7902 (tp30)
REVERT: B  221 GLU cc_start: 0.8180 (tt0) cc_final: 0.7530 (tt0)
REVERT: B  222 TYR cc_start: 0.7960 (m-80) cc_final: 0.7642 (m-10)
REVERT: B  292 MET cc_start: 0.8522 (mmm) cc_final: 0.8172 (mmt)
REVERT: B  330 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.7106 (mp)
REVERT: B  332 ARG cc_start: 0.4588 (mpt-90) cc_final: 0.1475 (mpt-90)
REVERT: B  370 LYS cc_start: 0.8558 (mppt) cc_final: 0.8223 (tptp)
REVERT: B  432 LYS cc_start: 0.8704 (mttm) cc_final: 0.8216 (mmtt)
REVERT: B  471 LEU cc_start: 0.8611 (pp) cc_final: 0.8396 (pp)
REVERT: B  496 ASN cc_start: 0.8841 (t0) cc_final: 0.8458 (t0)
REVERT: B  501 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6759 (mp10)
REVERT: B  516 PHE cc_start: 0.8553 (m-10) cc_final: 0.8175 (m-10)
REVERT: B  536 ARG cc_start: 0.6528 (ttt90) cc_final: 0.6230 (tpt-90)
REVERT: B  776 ASP cc_start: 0.7616 (p0) cc_final: 0.7324 (p0)
REVERT: B  788 TYR cc_start: 0.7995 (t80) cc_final: 0.7695 (t80)
REVERT: B  808 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7214 (mp10)
REVERT: B  922 TYR cc_start: 0.9112 (m-10) cc_final: 0.8262 (m-80)
REVERT: B  961 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8112 (pp)
REVERT: B 1040 PHE cc_start: 0.7669 (t80) cc_final: 0.7140 (t80)
REVERT: B 1058 MET cc_start: 0.8610 (mtm) cc_final: 0.8406 (mtt)
REVERT: B 1139 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8424 (tpt)
REVERT: B 1153 PHE cc_start: 0.8834 (t80) cc_final: 0.8595 (t80)
  outliers start: 101
  outliers final: 61
  residues processed: 456
  average time/residue: 0.1144
  time to fit residues: 84.0657
Evaluate side-chains
  437 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 367
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  131 GLU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  199 LEU
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  259 PHE
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1143 SER
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain A residue 1169 VAL
Chi-restraints excluded: chain C residue   28 ARG
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  102 LEU
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  436 ASP
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  501 GLN
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  739 HIS
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  808 GLN
Chi-restraints excluded: chain B residue  879 ASP
Chi-restraints excluded: chain B residue  961 LEU
Chi-restraints excluded: chain B residue  998 CYS
Chi-restraints excluded: chain B residue 1029 LEU
Chi-restraints excluded: chain B residue 1038 CYS
Chi-restraints excluded: chain B residue 1039 THR
Chi-restraints excluded: chain B residue 1139 MET
Chi-restraints excluded: chain B residue 1140 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 151 optimal weight:    0.9990
   chunk 187 optimal weight:    0.3980
   chunk 13 optimal weight:    0.0980
   chunk 133 optimal weight:    3.9990
   chunk 183 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    6.9990
   chunk 12 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 195 optimal weight:    4.9990
   chunk 155 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 837 ASN
B 839 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.123601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.106484 restraints weight = 39522.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.109344 restraints weight = 18622.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.111094 restraints weight = 11192.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.112350 restraints weight = 7944.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.112955 restraints weight = 6235.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.4849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  17074  Z= 0.133
  Angle     :  0.743  11.829  23204  Z= 0.359
  Chirality :  0.044   0.310   2632
  Planarity :  0.004   0.049   2921
  Dihedral  :  5.897  58.821   2310
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 23.32 %
    Favored  : 72.18 %
  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: -0.69 (0.19), residues: 2110
  helix:  0.83 (0.15), residues: 1158
  sheet: -1.64 (0.48), residues: 113
  loop : -2.17 (0.21), residues: 839

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 530 
 TYR   0.017   0.001   TYR A 224 
 PHE   0.029   0.001   PHE A 974 
 TRP   0.017   0.001   TRP A 337 
 HIS   0.005   0.001   HIS A 950 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (17069)
  covalent geometry    : angle       0.74314 (23196)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       0.59199 (    8)
  hydrogen bonds       : bond        0.03862 (  877)
  hydrogen bonds       : angle       4.70463 ( 2559)
  Misc. bond           : bond        0.00031 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  485 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 406
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.8396 (t0) cc_final: 0.8006 (p0)
REVERT: A  157 LEU cc_start: 0.8910 (mp) cc_final: 0.8519 (mt)
REVERT: A  216 MET cc_start: 0.7962 (mmm) cc_final: 0.7647 (mmm)
REVERT: A  240 LYS cc_start: 0.8316 (mtmm) cc_final: 0.8103 (mttt)
REVERT: A  294 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7904 (ptp90)
REVERT: A  428 ASP cc_start: 0.8461 (t70) cc_final: 0.7717 (t0)
REVERT: A  587 MET cc_start: 0.8008 (tmm) cc_final: 0.7674 (tmm)
REVERT: A  598 MET cc_start: 0.7605 (mpp) cc_final: 0.7281 (mmt)
REVERT: A  602 ARG cc_start: 0.7707 (mtt-85) cc_final: 0.7058 (mmt180)
REVERT: A  766 TYR cc_start: 0.8084 (t80) cc_final: 0.7845 (t80)
REVERT: A  886 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8456 (mm)
REVERT: A  961 LEU cc_start: 0.8295 (pt) cc_final: 0.8052 (pp)
REVERT: A  977 TYR cc_start: 0.8340 (m-10) cc_final: 0.8072 (m-80)
REVERT: A 1049 ASN cc_start: 0.8175 (m-40) cc_final: 0.7823 (m-40)
REVERT: A 1066 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8299 (mt-10)
REVERT: A 1122 MET cc_start: 0.8614 (mtt) cc_final: 0.8383 (mtt)
REVERT: B   93 TYR cc_start: 0.5589 (OUTLIER) cc_final: 0.4851 (t80)
REVERT: B  127 GLU cc_start: 0.8224 (tp30) cc_final: 0.7875 (tp30)
REVERT: B  216 MET cc_start: 0.8664 (mmm) cc_final: 0.8458 (tpt)
REVERT: B  221 GLU cc_start: 0.8244 (tt0) cc_final: 0.7653 (tt0)
REVERT: B  222 TYR cc_start: 0.7915 (m-80) cc_final: 0.7692 (m-10)
REVERT: B  242 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7580 (tp-100)
REVERT: B  332 ARG cc_start: 0.4570 (mpt-90) cc_final: 0.1443 (mpt-90)
REVERT: B  339 GLU cc_start: 0.7434 (pm20) cc_final: 0.7042 (pm20)
REVERT: B  340 GLU cc_start: 0.8108 (pm20) cc_final: 0.7726 (pm20)
REVERT: B  370 LYS cc_start: 0.8506 (mppt) cc_final: 0.8130 (tptp)
REVERT: B  432 LYS cc_start: 0.8663 (mttm) cc_final: 0.8192 (mmtt)
REVERT: B  447 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8252 (mp)
REVERT: B  464 LYS cc_start: 0.7387 (mttt) cc_final: 0.7073 (mttm)
REVERT: B  496 ASN cc_start: 0.8796 (t0) cc_final: 0.8429 (t0)
REVERT: B  501 GLN cc_start: 0.7506 (OUTLIER) cc_final: 0.6735 (mp10)
REVERT: B  536 ARG cc_start: 0.6520 (ttt90) cc_final: 0.6262 (tpt-90)
REVERT: B  776 ASP cc_start: 0.7489 (p0) cc_final: 0.7269 (p0)
REVERT: B  808 GLN cc_start: 0.7790 (OUTLIER) cc_final: 0.7096 (mp10)
REVERT: B  922 TYR cc_start: 0.9072 (m-10) cc_final: 0.8199 (m-80)
REVERT: B 1040 PHE cc_start: 0.7606 (t80) cc_final: 0.6989 (t80)
REVERT: B 1058 MET cc_start: 0.8505 (mtm) cc_final: 0.8293 (mtt)
REVERT: B 1128 ASP cc_start: 0.8256 (t70) cc_final: 0.7748 (t0)
  outliers start: 79
  outliers final: 53
  residues processed: 452
  average time/residue: 0.1131
  time to fit residues: 81.6593
Evaluate side-chains
  435 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 376
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  294 ARG
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  489 SER
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  508 LEU
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1143 SER
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  149 GLU
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  257 THR
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  501 GLN
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  737 GLU
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  808 GLN
Chi-restraints excluded: chain B residue  837 ASN
Chi-restraints excluded: chain B residue  842 LYS
Chi-restraints excluded: chain B residue  879 ASP
Chi-restraints excluded: chain B residue 1038 CYS
Chi-restraints excluded: chain B residue 1039 THR
Chi-restraints excluded: chain B residue 1100 VAL
Chi-restraints excluded: chain B residue 1140 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 167 optimal weight:    0.0980
   chunk 135 optimal weight:    6.9990
   chunk 114 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 196 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 61 optimal weight:    0.0980
   chunk 194 optimal weight:    0.5980
   chunk 4 optimal weight:   10.0000
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 310 ASN
A 576 GLN
A 929 ASN
C  69 ASN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 GLN
B 242 GLN
B 358 HIS
** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 ASN
B 837 ASN
B1099 HIS
B1166 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.124859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.107912 restraints weight = 39434.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.110747 restraints weight = 18680.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.112569 restraints weight = 11263.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.113627 restraints weight = 7973.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.114459 restraints weight = 6376.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start:          0.5119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  17074  Z= 0.130
  Angle     :  0.747  13.927  23204  Z= 0.358
  Chirality :  0.044   0.267   2632
  Planarity :  0.005   0.067   2921
  Dihedral  :  5.727  59.750   2310
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.54 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 24.46 %
    Favored  : 71.27 %
  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: -0.60 (0.19), residues: 2110
  helix:  0.84 (0.15), residues: 1167
  sheet: -1.57 (0.47), residues: 115
  loop : -2.07 (0.22), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B1113 
 TYR   0.024   0.001   TYR C  62 
 PHE   0.029   0.001   PHE A 974 
 TRP   0.025   0.001   TRP B1027 
 HIS   0.005   0.001   HIS A 950 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (17069)
  covalent geometry    : angle       0.74679 (23196)
  SS BOND              : bond        0.00255 (    4)
  SS BOND              : angle       0.65307 (    8)
  hydrogen bonds       : bond        0.03730 (  877)
  hydrogen bonds       : angle       4.70236 ( 2559)
  Misc. bond           : bond        0.00027 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  465 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 390
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.8330 (t0) cc_final: 0.7977 (p0)
REVERT: A  157 LEU cc_start: 0.8839 (mp) cc_final: 0.8468 (mt)
REVERT: A  204 TYR cc_start: 0.8466 (t80) cc_final: 0.7935 (t80)
REVERT: A  216 MET cc_start: 0.7831 (mmm) cc_final: 0.7546 (mmm)
REVERT: A  294 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7866 (ptp90)
REVERT: A  367 MET cc_start: 0.7793 (mtt) cc_final: 0.7590 (mmm)
REVERT: A  428 ASP cc_start: 0.8430 (t70) cc_final: 0.7711 (t0)
REVERT: A  457 MET cc_start: 0.8729 (mmm) cc_final: 0.8510 (mmm)
REVERT: A  542 LYS cc_start: 0.7636 (tttt) cc_final: 0.7430 (tptt)
REVERT: A  587 MET cc_start: 0.8170 (tmm) cc_final: 0.7793 (tmm)
REVERT: A  598 MET cc_start: 0.7582 (mpp) cc_final: 0.7253 (mmt)
REVERT: A  602 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7025 (mmt180)
REVERT: A  766 TYR cc_start: 0.8083 (t80) cc_final: 0.7874 (t80)
REVERT: A  886 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8450 (mm)
REVERT: A  961 LEU cc_start: 0.8288 (pt) cc_final: 0.8064 (pp)
REVERT: A 1028 LEU cc_start: 0.8984 (tp) cc_final: 0.8665 (tp)
REVERT: A 1049 ASN cc_start: 0.8149 (m-40) cc_final: 0.7826 (m-40)
REVERT: A 1066 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8361 (mt-10)
REVERT: A 1122 MET cc_start: 0.8599 (mtt) cc_final: 0.8315 (mtt)
REVERT: B   93 TYR cc_start: 0.5439 (OUTLIER) cc_final: 0.4633 (t80)
REVERT: B  127 GLU cc_start: 0.8212 (tp30) cc_final: 0.7881 (tp30)
REVERT: B  221 GLU cc_start: 0.8260 (tt0) cc_final: 0.7631 (tt0)
REVERT: B  242 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7603 (tp-100)
REVERT: B  292 MET cc_start: 0.8317 (mmm) cc_final: 0.8097 (mmt)
REVERT: B  332 ARG cc_start: 0.4552 (mpt-90) cc_final: 0.1443 (mpt-90)
REVERT: B  339 GLU cc_start: 0.7294 (pm20) cc_final: 0.6754 (pm20)
REVERT: B  340 GLU cc_start: 0.7845 (pm20) cc_final: 0.7213 (pm20)
REVERT: B  370 LYS cc_start: 0.8453 (mppt) cc_final: 0.8183 (tptp)
REVERT: B  432 LYS cc_start: 0.8636 (mttm) cc_final: 0.8166 (mmmt)
REVERT: B  496 ASN cc_start: 0.8825 (t0) cc_final: 0.8432 (t0)
REVERT: B  501 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6754 (mp10)
REVERT: B  536 ARG cc_start: 0.6416 (ttt90) cc_final: 0.6034 (tpt-90)
REVERT: B  776 ASP cc_start: 0.7535 (p0) cc_final: 0.7331 (p0)
REVERT: B  808 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7150 (mp10)
REVERT: B  922 TYR cc_start: 0.9045 (m-10) cc_final: 0.8145 (m-80)
REVERT: B  961 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8090 (pp)
REVERT: B 1040 PHE cc_start: 0.7526 (t80) cc_final: 0.6946 (t80)
  outliers start: 75
  outliers final: 53
  residues processed: 431
  average time/residue: 0.1143
  time to fit residues: 79.0512
Evaluate side-chains
  428 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 368
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  294 ARG
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  564 LEU
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1100 VAL
Chi-restraints excluded: chain A residue 1119 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1143 SER
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  242 GLN
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  439 VAL
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  501 GLN
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  808 GLN
Chi-restraints excluded: chain B residue  837 ASN
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  879 ASP
Chi-restraints excluded: chain B residue  961 LEU
Chi-restraints excluded: chain B residue 1036 LEU
Chi-restraints excluded: chain B residue 1038 CYS
Chi-restraints excluded: chain B residue 1039 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 127 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 135 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9990
   chunk 189 optimal weight:    7.9990
   chunk 47 optimal weight:    7.9990
   chunk 152 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 177 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 GLN
** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1099 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.125229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.107879 restraints weight = 39619.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.110709 restraints weight = 18964.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.112488 restraints weight = 11521.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.113701 restraints weight = 8197.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.114402 restraints weight = 6496.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.5250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  17074  Z= 0.138
  Angle     :  0.760  13.352  23204  Z= 0.363
  Chirality :  0.045   0.244   2632
  Planarity :  0.005   0.062   2921
  Dihedral  :  5.743  59.995   2310
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 13.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.63 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 25.20 %
    Favored  : 70.93 %
  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: -0.53 (0.19), residues: 2110
  helix:  0.87 (0.15), residues: 1161
  sheet: -1.41 (0.47), residues: 115
  loop : -2.00 (0.22), residues: 834

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  28 
 TYR   0.032   0.002   TYR B 222 
 PHE   0.044   0.002   PHE B1153 
 TRP   0.033   0.001   TRP B1027 
 HIS   0.006   0.001   HIS A 201 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (17069)
  covalent geometry    : angle       0.76033 (23196)
  SS BOND              : bond        0.00531 (    4)
  SS BOND              : angle       0.98317 (    8)
  hydrogen bonds       : bond        0.03746 (  877)
  hydrogen bonds       : angle       4.72380 ( 2559)
  Misc. bond           : bond        0.00029 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 372
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  156 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8052 (mm-40)
REVERT: A  157 LEU cc_start: 0.8873 (mp) cc_final: 0.8485 (mt)
REVERT: A  204 TYR cc_start: 0.8489 (t80) cc_final: 0.8019 (t80)
REVERT: A  216 MET cc_start: 0.7886 (mmm) cc_final: 0.7587 (mmm)
REVERT: A  294 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7875 (ptp90)
REVERT: A  367 MET cc_start: 0.8017 (mtt) cc_final: 0.7670 (mmm)
REVERT: A  428 ASP cc_start: 0.8460 (t70) cc_final: 0.7738 (t0)
REVERT: A  457 MET cc_start: 0.8705 (mmm) cc_final: 0.8474 (mmm)
REVERT: A  542 LYS cc_start: 0.7687 (tttt) cc_final: 0.7439 (tptt)
REVERT: A  587 MET cc_start: 0.8185 (tmm) cc_final: 0.7816 (tmm)
REVERT: A  598 MET cc_start: 0.7564 (mpp) cc_final: 0.7257 (mmt)
REVERT: A  602 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7049 (mmt180)
REVERT: A  766 TYR cc_start: 0.8074 (t80) cc_final: 0.7848 (t80)
REVERT: A  772 ARG cc_start: 0.7304 (mmm160) cc_final: 0.6976 (mmm160)
REVERT: A  886 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8461 (mm)
REVERT: A  961 LEU cc_start: 0.8332 (pt) cc_final: 0.8103 (pp)
REVERT: A 1049 ASN cc_start: 0.8206 (m-40) cc_final: 0.7879 (m-40)
REVERT: A 1066 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8425 (mt-10)
REVERT: A 1122 MET cc_start: 0.8559 (mtt) cc_final: 0.8341 (mtt)
REVERT: B   93 TYR cc_start: 0.5450 (OUTLIER) cc_final: 0.4638 (t80)
REVERT: B  127 GLU cc_start: 0.8260 (tp30) cc_final: 0.7936 (tp30)
REVERT: B  332 ARG cc_start: 0.4618 (mpt-90) cc_final: 0.1518 (mpt-90)
REVERT: B  339 GLU cc_start: 0.7313 (pm20) cc_final: 0.6881 (pm20)
REVERT: B  340 GLU cc_start: 0.7814 (pm20) cc_final: 0.7190 (pm20)
REVERT: B  370 LYS cc_start: 0.8483 (mppt) cc_final: 0.8240 (tptp)
REVERT: B  432 LYS cc_start: 0.8711 (mttm) cc_final: 0.8232 (mmmt)
REVERT: B  464 LYS cc_start: 0.7201 (mttt) cc_final: 0.6699 (mmtp)
REVERT: B  496 ASN cc_start: 0.8835 (t0) cc_final: 0.8465 (t0)
REVERT: B  501 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6780 (mp10)
REVERT: B  536 ARG cc_start: 0.6434 (ttt90) cc_final: 0.6060 (tpt-90)
REVERT: B  776 ASP cc_start: 0.7572 (p0) cc_final: 0.7357 (p0)
REVERT: B  788 TYR cc_start: 0.7940 (t80) cc_final: 0.7719 (t80)
REVERT: B  808 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7188 (mp10)
REVERT: B  922 TYR cc_start: 0.9048 (m-10) cc_final: 0.8060 (m-80)
REVERT: B  961 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8114 (pp)
REVERT: B 1040 PHE cc_start: 0.7537 (t80) cc_final: 0.6977 (t80)
REVERT: B 1128 ASP cc_start: 0.8236 (t70) cc_final: 0.7545 (t0)
REVERT: B 1146 ASP cc_start: 0.7509 (t0) cc_final: 0.7284 (m-30)
  outliers start: 68
  outliers final: 55
  residues processed: 411
  average time/residue: 0.1105
  time to fit residues: 73.5342
Evaluate side-chains
  420 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 359
  time to evaluate  : 0.611 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  294 ARG
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  340 GLU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1100 VAL
Chi-restraints excluded: chain A residue 1119 LEU
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1143 SER
Chi-restraints excluded: chain A residue 1159 LEU
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  241 LEU
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  501 GLN
Chi-restraints excluded: chain B residue  515 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  808 GLN
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  961 LEU
Chi-restraints excluded: chain B residue 1036 LEU
Chi-restraints excluded: chain B residue 1038 CYS
Chi-restraints excluded: chain B residue 1039 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 158 optimal weight:    0.4980
   chunk 65 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 179 optimal weight:   10.0000
   chunk 80 optimal weight:    0.8980
   chunk 143 optimal weight:    5.9990
   chunk 97 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 40 optimal weight:    9.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 283 ASN
** C  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 837 ASN
B1099 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.124216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.106913 restraints weight = 39621.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.109785 restraints weight = 18963.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.111606 restraints weight = 11426.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.112726 restraints weight = 8101.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.113283 restraints weight = 6443.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.5359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065  17074  Z= 0.146
  Angle     :  0.761  13.294  23204  Z= 0.365
  Chirality :  0.045   0.231   2632
  Planarity :  0.005   0.059   2921
  Dihedral  :  5.718  58.902   2310
  Min Nonbonded Distance : 1.834

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 25.77 %
    Favored  : 70.53 %
  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: -0.56 (0.19), residues: 2110
  helix:  0.84 (0.15), residues: 1178
  sheet: -1.35 (0.47), residues: 116
  loop : -2.05 (0.22), residues: 816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B1113 
 TYR   0.033   0.001   TYR B 222 
 PHE   0.030   0.002   PHE A 743 
 TRP   0.034   0.002   TRP B1027 
 HIS   0.005   0.001   HIS A 950 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (17069)
  covalent geometry    : angle       0.76111 (23196)
  SS BOND              : bond        0.00254 (    4)
  SS BOND              : angle       1.08257 (    8)
  hydrogen bonds       : bond        0.03747 (  877)
  hydrogen bonds       : angle       4.70330 ( 2559)
  Misc. bond           : bond        0.00028 (    1)

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

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

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4220 Ramachandran restraints generated.
    2110 Oldfield, 0 Emsley, 2110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 369
  time to evaluate  : 0.555 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.8421 (t0) cc_final: 0.8184 (p0)
REVERT: A  156 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8134 (mm-40)
REVERT: A  204 TYR cc_start: 0.8525 (t80) cc_final: 0.7996 (t80)
REVERT: A  216 MET cc_start: 0.7888 (mmm) cc_final: 0.7580 (mmm)
REVERT: A  428 ASP cc_start: 0.8486 (t70) cc_final: 0.7761 (t0)
REVERT: A  457 MET cc_start: 0.8738 (mmm) cc_final: 0.8518 (mmm)
REVERT: A  542 LYS cc_start: 0.7698 (tttt) cc_final: 0.7455 (tptt)
REVERT: A  587 MET cc_start: 0.8231 (tmm) cc_final: 0.7869 (tmm)
REVERT: A  598 MET cc_start: 0.7576 (mpp) cc_final: 0.7265 (mmt)
REVERT: A  602 ARG cc_start: 0.7700 (mtt-85) cc_final: 0.7050 (mmt180)
REVERT: A  766 TYR cc_start: 0.8094 (t80) cc_final: 0.7854 (t80)
REVERT: A  772 ARG cc_start: 0.7246 (mmm160) cc_final: 0.6958 (mmm160)
REVERT: A  886 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8479 (mm)
REVERT: A  961 LEU cc_start: 0.8344 (pt) cc_final: 0.8111 (pp)
REVERT: A 1049 ASN cc_start: 0.8240 (m-40) cc_final: 0.7888 (m-40)
REVERT: A 1066 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8370 (mt-10)
REVERT: A 1082 PRO cc_start: 0.9108 (Cg_exo) cc_final: 0.8863 (Cg_endo)
REVERT: A 1122 MET cc_start: 0.8585 (mtt) cc_final: 0.8355 (mtt)
REVERT: B   93 TYR cc_start: 0.5417 (OUTLIER) cc_final: 0.4576 (t80)
REVERT: B  126 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7732 (mm-30)
REVERT: B  127 GLU cc_start: 0.8295 (tp30) cc_final: 0.7956 (tp30)
REVERT: B  292 MET cc_start: 0.8391 (mmm) cc_final: 0.8141 (mmt)
REVERT: B  332 ARG cc_start: 0.4368 (mpt-90) cc_final: 0.1370 (mpt-90)
REVERT: B  339 GLU cc_start: 0.7316 (pm20) cc_final: 0.6868 (pm20)
REVERT: B  340 GLU cc_start: 0.7861 (pm20) cc_final: 0.7260 (pm20)
REVERT: B  370 LYS cc_start: 0.8499 (mppt) cc_final: 0.8272 (tptm)
REVERT: B  432 LYS cc_start: 0.8664 (mttm) cc_final: 0.8221 (mmmt)
REVERT: B  464 LYS cc_start: 0.7505 (mttt) cc_final: 0.7050 (mmtp)
REVERT: B  477 VAL cc_start: 0.8972 (t) cc_final: 0.8718 (p)
REVERT: B  496 ASN cc_start: 0.8847 (t0) cc_final: 0.8511 (t0)
REVERT: B  536 ARG cc_start: 0.6351 (ttt90) cc_final: 0.5937 (tpt-90)
REVERT: B  776 ASP cc_start: 0.7610 (p0) cc_final: 0.7398 (p0)
REVERT: B  788 TYR cc_start: 0.7828 (t80) cc_final: 0.7593 (t80)
REVERT: B  808 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7227 (mp10)
REVERT: B  922 TYR cc_start: 0.9054 (m-10) cc_final: 0.8044 (m-80)
REVERT: B  961 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8111 (pp)
REVERT: B 1040 PHE cc_start: 0.7554 (t80) cc_final: 0.7016 (t80)
REVERT: B 1146 ASP cc_start: 0.7467 (t0) cc_final: 0.7221 (m-30)
  outliers start: 65
  outliers final: 51
  residues processed: 405
  average time/residue: 0.1128
  time to fit residues: 73.8939
Evaluate side-chains
  414 residues out of total 1804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 359
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  179 LEU
Chi-restraints excluded: chain A residue  228 ILE
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  317 LEU
Chi-restraints excluded: chain A residue  335 MET
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  368 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  425 THR
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  499 THR
Chi-restraints excluded: chain A residue  515 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  583 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  778 THR
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1057 VAL
Chi-restraints excluded: chain A residue 1062 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1094 VAL
Chi-restraints excluded: chain A residue 1096 PHE
Chi-restraints excluded: chain A residue 1100 VAL
Chi-restraints excluded: chain A residue 1121 HIS
Chi-restraints excluded: chain A residue 1143 SER
Chi-restraints excluded: chain C residue   47 PHE
Chi-restraints excluded: chain C residue   56 LEU
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain B residue   93 TYR
Chi-restraints excluded: chain B residue  199 LEU
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain B residue  213 THR
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  262 LEU
Chi-restraints excluded: chain B residue  287 VAL
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  493 ILE
Chi-restraints excluded: chain B residue  500 THR
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  583 PHE
Chi-restraints excluded: chain B residue  765 LEU
Chi-restraints excluded: chain B residue  808 GLN
Chi-restraints excluded: chain B residue  837 ASN
Chi-restraints excluded: chain B residue  842 LYS
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  961 LEU
Chi-restraints excluded: chain B residue 1036 LEU
Chi-restraints excluded: chain B residue 1038 CYS
Chi-restraints excluded: chain B residue 1039 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 210
   random chunks:
   chunk 134 optimal weight:   10.0000
   chunk 7 optimal weight:    4.9990
   chunk 158 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 199 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 169 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 146 optimal weight:    3.9990
   chunk 196 optimal weight:    8.9990
   chunk 200 optimal weight:   10.0000
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 177 GLN
A 274 GLN
** A 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 177 GLN
** B 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 576 GLN
B 837 ASN
** B 950 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1099 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.118490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.100839 restraints weight = 40063.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.103616 restraints weight = 19448.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.105387 restraints weight = 11873.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.106392 restraints weight = 8503.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.106966 restraints weight = 6877.351|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067  17074  Z= 0.244
  Angle     :  0.830  12.342  23204  Z= 0.405
  Chirality :  0.048   0.207   2632
  Planarity :  0.005   0.059   2921
  Dihedral  :  5.970  53.802   2310
  Min Nonbonded Distance : 1.745

Molprobity Statistics.
  All-atom Clashscore : 15.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 26.34 %
    Favored  : 70.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.62 (0.19), residues: 2110
  helix:  0.78 (0.15), residues: 1172
  sheet: -1.35 (0.49), residues: 116
  loop : -2.05 (0.22), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B1113 
 TYR   0.034   0.002   TYR B 222 
 PHE   0.036   0.002   PHE B1153 
 TRP   0.044   0.002   TRP B1027 
 HIS   0.007   0.001   HIS A 950 

Details of bonding type rmsd
  covalent geometry    : bond        0.00564 (17069)
  covalent geometry    : angle       0.83022 (23196)
  SS BOND              : bond        0.00431 (    4)
  SS BOND              : angle       1.36368 (    8)
  hydrogen bonds       : bond        0.04150 (  877)
  hydrogen bonds       : angle       4.89800 ( 2559)
  Misc. bond           : bond        0.00056 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3113.50 seconds
wall clock time: 54 minutes 31.77 seconds (3271.77 seconds total)