Starting phenix.real_space_refine
on Mon May 19 17:44:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7jpv_22424/05_2025/7jpv_22424.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7jpv_22424/05_2025/7jpv_22424.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7jpv_22424/05_2025/7jpv_22424.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7jpv_22424/05_2025/7jpv_22424.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7jpv_22424/05_2025/7jpv_22424.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7jpv_22424/05_2025/7jpv_22424.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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      1      9.91       5
     P      10      5.49       5
     S     107      5.16       5
     C   11930      2.51       5
     N    2940      2.21       5
     O    3300      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 162 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 18288
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 8987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1115, 8987
          Classifications: {'peptide': 1115}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 36, 'TRANS': 1078}
          Chain breaks: 10
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "E"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1080
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 6, 'TRANS': 132}
          Chain breaks: 2
    Chain: "F"
      Number of atoms: 7804
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 973, 7796
          Classifications: {'peptide': 973}
          Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 973, 7796
          Classifications: {'peptide': 973}
          Link IDs: {'PCIS': 2, 'PTRANS': 43, 'TRANS': 927}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 7954
    Chain: "A"
      Number of atoms: 363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 363
          Unusual residues: {' CA': 1, '3PE': 9}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 97
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'3PE:plan-1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "E"
      Number of atoms: 54
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 54
          Unusual residues: {'PC1': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 13.28, per 1000 atoms: 0.73
  Number of scatterers: 18288
  At special positions: 0
  Unit cell: (144.82, 141.478, 158.188, 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)
     Ca      1     19.99
     S     107     16.00
     P      10     15.00
     O    3300      8.00
     N    2940      7.00
     C   11930      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 226 " - pdb=" SG  CYS A 254 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 245 " - pdb=" SG  CYS A 261 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 957 " - pdb=" SG  CYS A 968 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1338 " - pdb=" SG  CYS A1352 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 305 " - pdb=" SG  CYS F1047 " distance=2.04
    Simple disulfide: pdb=" SG  CYS F 356 " - pdb=" SG  CYS F1062 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 406 " - pdb=" SG  CYS F1074 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 670 " - pdb=" SG  CYS F 700 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 844 " - pdb=" SG  CYS F 853 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 907 " - pdb=" SG  CYS F 977 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 999 " - pdb=" SG  CYS F1029 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F1002 " - pdb=" SG  CYS F1027 " 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=5, symmetry=0
  Number of additional bonds: simple=5, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 4.62
  Conformation dependent library (CDL) restraints added in 3.0 seconds
  

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4218

  Finding SS restraints...
    Secondary structure from input PDB file:
      92 helices and 16 sheets defined
      53.4% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 65
    Processing helix  chain 'A' and resid 80 through 106
      removed outlier: 3.599A  pdb=" N   LYS A  88 " --> pdb=" O   LEU A  84 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   TYR A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ILE A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 143
      removed outlier: 3.849A  pdb=" N   GLN A 141 " --> pdb=" O   ALA A 137 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ASN A 143 " --> pdb=" O   LEU A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 166
    Processing helix  chain 'A' and resid 167 through 171
      removed outlier: 3.719A  pdb=" N   ARG A 171 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 179
      removed outlier: 3.670A  pdb=" N   VAL A 176 " --> pdb=" O   PRO A 172 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 193
      removed outlier: 3.907A  pdb=" N   GLN A 183 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   VAL A 184 " --> pdb=" O   PRO A 180 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   VAL A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 218
    Processing helix  chain 'A' and resid 277 through 290
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.687A  pdb=" N   VAL A 297 " --> pdb=" O   GLY A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 346
      removed outlier: 4.284A  pdb=" N   PHE A 314 " --> pdb=" O   PRO A 310 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   PHE A 324 " --> pdb=" O   LEU A 320 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ILE A 325 " --> pdb=" O   GLY A 321 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU A 326 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 450
      removed outlier: 4.296A  pdb=" N   ILE A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 487
      removed outlier: 3.553A  pdb=" N   THR A 461 " --> pdb=" O   PRO A 457 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE A 466 " --> pdb=" O   HIS A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 491
      removed outlier: 3.780A  pdb=" N   TYR A 491 " --> pdb=" O   LEU A 488 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 488 through 491'
    Processing helix  chain 'A' and resid 494 through 498
    Processing helix  chain 'A' and resid 499 through 515
    Processing helix  chain 'A' and resid 520 through 530
      removed outlier: 3.569A  pdb=" N   ILE A 524 " --> pdb=" O   THR A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 535
      removed outlier: 3.823A  pdb=" N   LEU A 535 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 542
      removed outlier: 3.654A  pdb=" N   TRP A 542 " --> pdb=" O   ILE A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 582
      removed outlier: 5.719A  pdb=" N   SER A 561 " --> pdb=" O   ARG A 557 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   LEU A 562 " --> pdb=" O   SER A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 612
    Processing helix  chain 'A' and resid 615 through 627
      removed outlier: 3.523A  pdb=" N   VAL A 619 " --> pdb=" O   ASP A 615 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   TYR A 621 " --> pdb=" O   ASN A 617 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN A 622 " --> pdb=" O   SER A 618 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLY A 623 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   TYR A 627 " --> pdb=" O   GLY A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 636
      removed outlier: 4.052A  pdb=" N   LEU A 636 " --> pdb=" O   TYR A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 647
    Processing helix  chain 'A' and resid 647 through 657
      removed outlier: 3.649A  pdb=" N   ILE A 651 " --> pdb=" O   CYS A 647 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU A 652 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 673
      removed outlier: 3.639A  pdb=" N   ALA A 667 " --> pdb=" O   ASN A 663 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLU A 668 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 811
      removed outlier: 3.639A  pdb=" N   LEU A 807 " --> pdb=" O   ASN A 803 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE A 809 " --> pdb=" O   ILE A 805 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU A 810 " --> pdb=" O   LEU A 806 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU A 811 " --> pdb=" O   LEU A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 818
      removed outlier: 3.746A  pdb=" N   ALA A 817 " --> pdb=" O   SER A 813 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ALA A 818 " --> pdb=" O   ALA A 814 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 813 through 818'
    Processing helix  chain 'A' and resid 828 through 852
      removed outlier: 3.716A  pdb=" N   ALA A 838 " --> pdb=" O   TYR A 834 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   PHE A 843 " --> pdb=" O   PHE A 839 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLU A 846 " --> pdb=" O   VAL A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 881
      removed outlier: 4.176A  pdb=" N   SER A 879 " --> pdb=" O   VAL A 875 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LEU A 880 " --> pdb=" O   VAL A 876 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ILE A 881 " --> pdb=" O   ALA A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 899
      removed outlier: 3.997A  pdb=" N   ARG A 897 " --> pdb=" O   VAL A 893 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL A 898 " --> pdb=" O   LYS A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 907 through 912
      removed outlier: 3.776A  pdb=" N   LYS A 912 " --> pdb=" O   ILE A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 928
      removed outlier: 4.068A  pdb=" N   VAL A 917 " --> pdb=" O   GLY A 913 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A 926 " --> pdb=" O   PHE A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 950
      removed outlier: 4.044A  pdb=" N   VAL A 934 " --> pdb=" O   ASN A 930 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 977 through 979
      No H-bonds generated for 'chain 'A' and resid 977 through 979'
    Processing helix  chain 'A' and resid 999 through 1012
    Processing helix  chain 'A' and resid 1015 through 1024
      removed outlier: 3.653A  pdb=" N   LEU A1019 " --> pdb=" O   GLY A1015 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ARG A1022 " --> pdb=" O   GLN A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1043 through 1048
      removed outlier: 3.548A  pdb=" N   TYR A1048 " --> pdb=" O   PHE A1044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1072
      removed outlier: 3.504A  pdb=" N   VAL A1064 " --> pdb=" O   PHE A1060 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1095
      removed outlier: 3.977A  pdb=" N   VAL A1089 " --> pdb=" O   GLN A1085 " (cutoff:3.500A)
      removed outlier: 5.382A  pdb=" N   GLN A1090 " --> pdb=" O   ARG A1086 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ALA A1095 " --> pdb=" O   TYR A1091 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1105 through 1116
      removed outlier: 4.890A  pdb=" N   VAL A1111 " --> pdb=" O   TYR A1107 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   VAL A1114 " --> pdb=" O   GLN A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1117 through 1137
      removed outlier: 3.710A  pdb=" N   GLU A1121 " --> pdb=" O   SER A1117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1152 through 1171
    Processing helix  chain 'A' and resid 1180 through 1206
    Processing helix  chain 'A' and resid 1232 through 1235
    Processing helix  chain 'A' and resid 1236 through 1241
      removed outlier: 4.112A  pdb=" N   VAL A1240 " --> pdb=" O   ARG A1236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1242 through 1249
      removed outlier: 3.945A  pdb=" N   LYS A1245 " --> pdb=" O   ARG A1242 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ARG A1249 " --> pdb=" O   LEU A1246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1262
      removed outlier: 3.901A  pdb=" N   THR A1255 " --> pdb=" O   GLU A1251 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU A1256 " --> pdb=" O   GLY A1252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1269 through 1289
      removed outlier: 3.806A  pdb=" N   ILE A1274 " --> pdb=" O   VAL A1270 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A1275 " --> pdb=" O   ALA A1271 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL A1283 " --> pdb=" O   PHE A1279 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ILE A1284 " --> pdb=" O   ILE A1280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1308 through 1322
    Processing helix  chain 'A' and resid 1324 through 1332
      removed outlier: 3.557A  pdb=" N   ILE A1328 " --> pdb=" O   ALA A1324 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU A1330 " --> pdb=" O   GLN A1326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1356 through 1381
      removed outlier: 3.669A  pdb=" N   ILE A1362 " --> pdb=" O   TYR A1358 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   SER A1363 " --> pdb=" O   TYR A1359 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A1379 " --> pdb=" O   LEU A1375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1383 through 1388
    Processing helix  chain 'A' and resid 1395 through 1410
      removed outlier: 3.552A  pdb=" N   LEU A1399 " --> pdb=" O   GLY A1395 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A1407 " --> pdb=" O   LYS A1403 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU A1408 " --> pdb=" O   ALA A1404 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   TYR A1409 " --> pdb=" O   ILE A1405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1425 through 1429
    Processing helix  chain 'E' and resid 6 through 29
      removed outlier: 3.577A  pdb=" N   VAL E  18 " --> pdb=" O   PHE E  14 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 127
      removed outlier: 3.867A  pdb=" N   CYS E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   MET E 127 " --> pdb=" O   ILE E 123 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 129 through 135
      removed outlier: 3.538A  pdb=" N   LYS E 132 " --> pdb=" O   PHE E 129 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   ASP E 134 " --> pdb=" O   LYS E 131 " (cutoff:3.500A)
      removed outlier: 5.188A  pdb=" N   TYR E 135 " --> pdb=" O   LYS E 132 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 136 through 163
      removed outlier: 3.583A  pdb=" N   SER E 141 " --> pdb=" O   LEU E 137 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   MET E 142 " --> pdb=" O   ARG E 138 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   VAL E 153 " --> pdb=" O   LEU E 149 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 179 through 204
      removed outlier: 3.741A  pdb=" N   VAL E 190 " --> pdb=" O   CYS E 186 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 29 through 51
      removed outlier: 3.570A  pdb=" N   THR F  46 " --> pdb=" O   GLU F  42 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 53 through 64
      removed outlier: 3.617A  pdb=" N   GLU F  62 " --> pdb=" O   VAL F  58 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   TYR F  64 " --> pdb=" O   ILE F  60 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 76 through 110
      removed outlier: 3.680A  pdb=" N   LEU F  97 " --> pdb=" O   ARG F  93 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ARG F  99 " --> pdb=" O   LYS F  95 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   LEU F 100 " --> pdb=" O   ALA F  96 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA F 110 " --> pdb=" O   LYS F 106 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 178 through 188
      removed outlier: 3.506A  pdb=" N   ASN F 183 " --> pdb=" O   THR F 179 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   GLU F 184 " --> pdb=" O   ILE F 180 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR F 188 " --> pdb=" O   GLU F 184 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 191 through 202
    Processing helix  chain 'F' and resid 239 through 242
    Processing helix  chain 'F' and resid 243 through 250
    Processing helix  chain 'F' and resid 263 through 267
    Processing helix  chain 'F' and resid 268 through 283
      removed outlier: 3.629A  pdb=" N   LYS F 272 " --> pdb=" O   GLY F 268 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR F 276 " --> pdb=" O   LYS F 272 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLU F 283 " --> pdb=" O   SER F 279 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 313 through 325
    Processing helix  chain 'F' and resid 334 through 346
      removed outlier: 3.710A  pdb=" N   GLY F 338 " --> pdb=" O   ASP F 334 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 371 through 379
      removed outlier: 3.547A  pdb=" N   PHE F 375 " --> pdb=" O   ALA F 371 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 398 through 408
      removed outlier: 3.516A  pdb=" N   GLN F 402 " --> pdb=" O   ARG F 398 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 418 through 422
      removed outlier: 3.521A  pdb=" N   ILE F 421 " --> pdb=" O   ILE F 418 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ARG F 422 " --> pdb=" O   GLY F 419 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 418 through 422'
    Processing helix  chain 'F' and resid 428 through 433
    Processing helix  chain 'F' and resid 433 through 438
    Processing helix  chain 'F' and resid 496 through 501
      removed outlier: 3.655A  pdb=" N   LYS F 500 " --> pdb=" O   LEU F 496 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 542 through 546
      removed outlier: 3.620A  pdb=" N   LYS F 545 " --> pdb=" O   ASN F 542 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 562 through 566
    Processing helix  chain 'F' and resid 572 through 582
      removed outlier: 4.332A  pdb=" N   ASP F 582 " --> pdb=" O   ASN F 578 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 640 through 649
    Processing helix  chain 'F' and resid 650 through 651
      No H-bonds generated for 'chain 'F' and resid 650 through 651'
    Processing helix  chain 'F' and resid 652 through 654
      No H-bonds generated for 'chain 'F' and resid 652 through 654'
    Processing helix  chain 'F' and resid 655 through 660
    Processing helix  chain 'F' and resid 678 through 693
      removed outlier: 3.545A  pdb=" N   ARG F 692 " --> pdb=" O   GLU F 688 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 701 through 722
      removed outlier: 3.702A  pdb=" N   ILE F 705 " --> pdb=" O   ASN F 701 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 748 through 753
      removed outlier: 3.936A  pdb=" N   GLU F 753 " --> pdb=" O   LYS F 749 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 764 through 773
    Processing helix  chain 'F' and resid 820 through 830
    Processing helix  chain 'F' and resid 877 through 882
      removed outlier: 3.677A  pdb=" N   ILE F 881 " --> pdb=" O   PHE F 877 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 882 through 892
    Processing helix  chain 'F' and resid 1045 through 1049
      removed outlier: 3.540A  pdb=" N   ASP F1048 " --> pdb=" O   ASP F1045 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 228
      removed outlier: 3.916A  pdb=" N   THR A 225 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ARG A 262 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 955 through 956
    Processing sheet with id=AA3, first strand: chain 'A' and resid 971 through 975
    Processing sheet with id=AA4, first strand: chain 'F' and resid 68 through 72
    Processing sheet with id=AA5, first strand: chain 'F' and resid 144 through 146
      removed outlier: 6.122A  pdb=" N   VAL F 124 " --> pdb=" O   GLN F 145 " (cutoff:3.500A)
      removed outlier: 9.531A  pdb=" N   VAL F 168 " --> pdb=" O   VAL F 125 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   TYR F 127 " --> pdb=" O   VAL F 168 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'F' and resid 152 through 153
    Processing sheet with id=AA7, first strand: chain 'F' and resid 217 through 220
      removed outlier: 3.826A  pdb=" N   GLY F 488 " --> pdb=" O   VAL F 468 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 217 through 220
      removed outlier: 3.826A  pdb=" N   GLY F 488 " --> pdb=" O   VAL F 468 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 300 through 302
      removed outlier: 6.193A  pdb=" N   ILE F 360 " --> pdb=" O   PHE F 387 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   PHE F 389 " --> pdb=" O   ILE F 360 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   LEU F 362 " --> pdb=" O   PHE F 389 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   VAL F 391 " --> pdb=" O   LEU F 362 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   THR F 364 " --> pdb=" O   VAL F 391 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   TYR F 411 " --> pdb=" O   VAL F 386 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'F' and resid 523 through 525
      removed outlier: 6.159A  pdb=" N   ALA F 516 " --> pdb=" O   LEU F 524 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   PHE F 515 " --> pdb=" O   ALA F 623 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU F 624 " --> pdb=" O   THR F 610 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU F 626 " --> pdb=" O   THR F 608 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY F 586 " --> pdb=" O   TRP F 611 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 661 through 663
      removed outlier: 3.941A  pdb=" N   THR F 744 " --> pdb=" O   PHE F 663 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE F 736 " --> pdb=" O   GLY F 816 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   LYS F 818 " --> pdb=" O   LYS F 733 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 661 through 663
      removed outlier: 3.941A  pdb=" N   THR F 744 " --> pdb=" O   PHE F 663 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE F 736 " --> pdb=" O   GLY F 816 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   MET F 796 " --> pdb=" O   THR F 779 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 803 through 804
    Processing sheet with id=AB5, first strand: chain 'F' and resid 862 through 864
      removed outlier: 6.664A  pdb=" N   ILE F 855 " --> pdb=" O   LEU F 863 " (cutoff:3.500A)
      removed outlier: 6.033A  pdb=" N   ILE F1005 " --> pdb=" O   GLU F1022 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 895 through 897
    Processing sheet with id=AB7, first strand: chain 'F' and resid 900 through 907
      removed outlier: 5.655A  pdb=" N   TYR F 901 " --> pdb=" O   GLN F 981 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   GLN F 981 " --> pdb=" O   TYR F 901 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   TYR F 903 " --> pdb=" O   THR F 979 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   THR F 979 " --> pdb=" O   TYR F 903 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   ILE F 978 " --> pdb=" O   SER F1041 " (cutoff:3.500A)

    854 hydrogen bonds defined for protein.
    2459 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: 6.21

  Time building geometry restraints manager: 5.37 seconds

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

  Histogram of bond lengths:
        1.04 -     1.20: 1
        1.20 -     1.36: 5702
        1.36 -     1.51: 6507
        1.51 -     1.67: 6312
        1.67 -     1.83: 166
  Bond restraints: 18688
  Sorted by residual:
  bond pdb=" C   ASN A1036 "
       pdb=" N   ASN A1037 "
    ideal  model  delta    sigma   weight residual
    1.334  1.044  0.290 1.27e-02 6.20e+03 5.21e+02
  bond pdb=" C21 3PE A1908 "
       pdb=" O21 3PE A1908 "
    ideal  model  delta    sigma   weight residual
    1.316  1.455 -0.139 2.00e-02 2.50e+03 4.80e+01
  bond pdb=" C21 3PE A1902 "
       pdb=" O21 3PE A1902 "
    ideal  model  delta    sigma   weight residual
    1.316  1.454 -0.138 2.00e-02 2.50e+03 4.78e+01
  bond pdb=" C21 3PE A1905 "
       pdb=" O21 3PE A1905 "
    ideal  model  delta    sigma   weight residual
    1.316  1.453 -0.137 2.00e-02 2.50e+03 4.73e+01
  bond pdb=" C21 3PE A1906 "
       pdb=" O21 3PE A1906 "
    ideal  model  delta    sigma   weight residual
    1.316  1.453 -0.137 2.00e-02 2.50e+03 4.69e+01
  ... (remaining 18683 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.05: 24629
        2.05 -     4.11: 510
        4.11 -     6.16: 87
        6.16 -     8.21: 9
        8.21 -    10.27: 25
  Bond angle restraints: 25260
  Sorted by residual:
  angle pdb=" N   GLY A1062 "
        pdb=" CA  GLY A1062 "
        pdb=" C   GLY A1062 "
      ideal   model   delta    sigma   weight residual
     112.77  107.77    5.00 1.28e+00 6.10e-01 1.52e+01
  angle pdb=" N   ILE A1052 "
        pdb=" CA  ILE A1052 "
        pdb=" C   ILE A1052 "
      ideal   model   delta    sigma   weight residual
     110.36  114.20   -3.84 1.05e+00 9.07e-01 1.34e+01
  angle pdb=" N   LEU A 937 "
        pdb=" CA  LEU A 937 "
        pdb=" C   LEU A 937 "
      ideal   model   delta    sigma   weight residual
     112.45  107.54    4.91 1.39e+00 5.18e-01 1.25e+01
  angle pdb=" N   PHE A1060 "
        pdb=" CA  PHE A1060 "
        pdb=" C   PHE A1060 "
      ideal   model   delta    sigma   weight residual
     112.23  107.80    4.43 1.26e+00 6.30e-01 1.24e+01
  angle pdb=" C2  3PE A1903 "
        pdb=" O21 3PE A1903 "
        pdb=" C21 3PE A1903 "
      ideal   model   delta    sigma   weight residual
     121.04  110.77   10.27 3.00e+00 1.11e-01 1.17e+01
  ... (remaining 25255 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.05: 10045
       23.05 -    46.09: 962
       46.09 -    69.14: 223
       69.14 -    92.18: 38
       92.18 -   115.23: 3
  Dihedral angle restraints: 11271
    sinusoidal: 4741
      harmonic: 6530
  Sorted by residual:
  dihedral pdb=" CB  CYS F 999 "
           pdb=" SG  CYS F 999 "
           pdb=" SG  CYS F1029 "
           pdb=" CB  CYS F1029 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.32  -88.68     1      1.00e+01 1.00e-02 9.38e+01
  dihedral pdb=" CB  CYS F 670 "
           pdb=" SG  CYS F 670 "
           pdb=" SG  CYS F 700 "
           pdb=" CB  CYS F 700 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -158.79   72.79     1      1.00e+01 1.00e-02 6.76e+01
  dihedral pdb=" CB  CYS A 226 "
           pdb=" SG  CYS A 226 "
           pdb=" SG  CYS A 254 "
           pdb=" CB  CYS A 254 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.60  -68.60     1      1.00e+01 1.00e-02 6.10e+01
  ... (remaining 11268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1954
       0.040 -    0.080: 682
       0.080 -    0.121: 154
       0.121 -    0.161: 24
       0.161 -    0.201: 3
  Chirality restraints: 2817
  Sorted by residual:
  chirality pdb=" CA  PHE A 314 "
            pdb=" N   PHE A 314 "
            pdb=" C   PHE A 314 "
            pdb=" CB  PHE A 314 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CA  VAL A1034 "
            pdb=" N   VAL A1034 "
            pdb=" C   VAL A1034 "
            pdb=" CB  VAL A1034 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.64   -0.20 2.00e-01 2.50e+01 9.72e-01
  chirality pdb=" CA  GLU A  76 "
            pdb=" N   GLU A  76 "
            pdb=" C   GLU A  76 "
            pdb=" CB  GLU A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.34e-01
  ... (remaining 2814 not shown)

  Planarity restraints: 3153
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A  51 "    0.040 5.00e-02 4.00e+02   6.11e-02 5.97e+00
        pdb=" N   PRO A  52 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A  52 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A  52 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU F 141 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO F 142 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO F 142 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO F 142 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 300 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.09e+00
        pdb=" C   TRP A 300 "    0.035 2.00e-02 2.50e+03
        pdb=" O   TRP A 300 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 301 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 3150 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 207
        2.61 -     3.18: 16162
        3.18 -     3.76: 26683
        3.76 -     4.33: 38099
        4.33 -     4.90: 63469
  Nonbonded interactions: 144620
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 210 "
            pdb=" OH  TYR A 313 "
     model   vdw
     2.040 3.040
  nonbonded pdb=" N   3PE A1910 "
            pdb=" O14 3PE A1910 "
     model   vdw
     2.079 3.120
  nonbonded pdb=" N   3PE A1903 "
            pdb=" O14 3PE A1903 "
     model   vdw
     2.080 3.120
  nonbonded pdb=" OD2 ASP F 154 "
            pdb=" OH  TYR F 163 "
     model   vdw
     2.100 3.040
  nonbonded pdb=" O   TYR F  61 "
            pdb=" OH  TYR F  68 "
     model   vdw
     2.135 3.040
  ... (remaining 144615 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.720
  Check model and map are aligned:         0.140
  Set scattering table:                    0.180
  Process input model:                     44.070
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.070
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   49.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
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      :  0.012   0.884  18705  Z= 1.099
  Angle     :  0.757  10.266  25284  Z= 0.386
  Chirality :  0.042   0.201   2817
  Planarity :  0.004   0.061   3153
  Dihedral  : 18.503 115.231   7017
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 13.82
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.57 %
    Favored  : 93.25 %
  Rotamer:
    Outliers :  7.64 %
    Allowed  : 20.88 %
    Favored  : 71.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.99 (0.15), residues: 2194
  helix: -1.82 (0.13), residues: 1070
  sheet: -2.70 (0.33), residues: 192
  loop : -3.62 (0.17), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP F 187 
 HIS   0.003   0.001   HIS F 888 
 PHE   0.016   0.001   PHE F 157 
 TYR   0.016   0.001   TYR A1109 
 ARG   0.003   0.000   ARG F 769 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16517 (  831)
  hydrogen bonds       : angle       6.67026 ( 2459)
  SS BOND              : bond        0.00374 (   12)
  SS BOND              : angle       1.44121 (   24)
  covalent geometry    : bond        0.00628 (18688)
  covalent geometry    : angle       0.75573 (25260)
  Misc. bond           : bond        0.64095 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  432 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 150
    poor density    : 282
  time to evaluate  : 1.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 PHE cc_start: 0.8495 (t80) cc_final: 0.8249 (t80)
REVERT: A  343 LYS cc_start: 0.5271 (ptpp) cc_final: 0.5063 (pttt)
REVERT: A  828 ARG cc_start: 0.4607 (ttp-170) cc_final: 0.4278 (tpp-160)
REVERT: A  938 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8109 (mp)
REVERT: A 1040 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7723 (pm20)
REVERT: A 1060 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.6656 (t80)
REVERT: A 1186 ASP cc_start: 0.8159 (t0) cc_final: 0.7872 (t0)
REVERT: A 1205 PHE cc_start: 0.4638 (t80) cc_final: 0.4438 (t80)
REVERT: A 1316 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8752 (mp)
REVERT: A 1381 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6293 (tmm)
REVERT: E  189 PHE cc_start: 0.7287 (t80) cc_final: 0.6984 (t80)
REVERT: F  281 MET cc_start: 0.8844 (tpp) cc_final: 0.8426 (ttm)
REVERT: F  348 ASN cc_start: 0.8484 (OUTLIER) cc_final: 0.8271 (t0)
REVERT: F  368 GLU cc_start: 0.7367 (pt0) cc_final: 0.7133 (pt0)
REVERT: F  380 LYS cc_start: 0.8418 (ttpp) cc_final: 0.7895 (ttpt)
REVERT: F  413 TYR cc_start: 0.9275 (m-80) cc_final: 0.8964 (m-80)
REVERT: F  442 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8386 (ttpt)
REVERT: F  604 LYS cc_start: 0.8378 (mtmm) cc_final: 0.8132 (mttm)
REVERT: F  858 ASP cc_start: 0.7959 (p0) cc_final: 0.7630 (p0)
  outliers start: 150
  outliers final: 112
  residues processed: 410
  average time/residue: 0.2985
  time to fit residues: 185.3673
Evaluate side-chains
  361 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 118
    poor density    : 243
  time to evaluate  : 2.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   65 CYS
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  315 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  468 ASN
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  510 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  547 ASN
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  792 CYS
Chi-restraints excluded: chain A residue  804 PHE
Chi-restraints excluded: chain A residue  819 GLU
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  925 ILE
Chi-restraints excluded: chain A residue  931 ILE
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue  938 LEU
Chi-restraints excluded: chain A residue  964 THR
Chi-restraints excluded: chain A residue  999 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1011 SER
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1038 ARG
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1040 GLU
Chi-restraints excluded: chain A residue 1041 MET
Chi-restraints excluded: chain A residue 1047 ILE
Chi-restraints excluded: chain A residue 1050 ILE
Chi-restraints excluded: chain A residue 1052 ILE
Chi-restraints excluded: chain A residue 1054 PHE
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1060 PHE
Chi-restraints excluded: chain A residue 1067 THR
Chi-restraints excluded: chain A residue 1069 GLN
Chi-restraints excluded: chain A residue 1082 ASP
Chi-restraints excluded: chain A residue 1093 LEU
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1159 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1198 ILE
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1255 THR
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1316 LEU
Chi-restraints excluded: chain A residue 1380 ILE
Chi-restraints excluded: chain A residue 1381 MET
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain E residue   27 VAL
Chi-restraints excluded: chain E residue  157 VAL
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain F residue   32 THR
Chi-restraints excluded: chain F residue   59 ASP
Chi-restraints excluded: chain F residue   94 SER
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  181 VAL
Chi-restraints excluded: chain F residue  205 LEU
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain F residue  270 THR
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  348 ASN
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  465 THR
Chi-restraints excluded: chain F residue  478 LYS
Chi-restraints excluded: chain F residue  479 THR
Chi-restraints excluded: chain F residue  552 ASN
Chi-restraints excluded: chain F residue  594 VAL
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  729 ILE
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  798 SER
Chi-restraints excluded: chain F residue  815 VAL
Chi-restraints excluded: chain F residue  817 ILE
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  853 CYS
Chi-restraints excluded: chain F residue  874 ILE
Chi-restraints excluded: chain F residue  997 LEU
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1014 THR
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1068 LEU
Chi-restraints excluded: chain F residue 1074 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 221
   random chunks:
   chunk 186 optimal weight:    6.9990
   chunk 167 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 112 optimal weight:    5.9990
   chunk 89 optimal weight:    1.9990
   chunk 173 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 128 optimal weight:    0.9990
   chunk 200 optimal weight:    3.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 307 ASN
A 327 ASN
A 453 HIS
A 547 ASN
A 599 ASN
A 797 ASN
A 948 GLN
A1085 GLN
A1108 GLN
A1138 GLN
A1154 ASN
F  65 GLN
F  74 ASN
F 307 GLN
** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 484 GLN
F 511 ASN
F 552 ASN
F 644 GLN
F 679 ASN
F 685 ASN
F 866 ASN
F 981 GLN
F 983 GLN
F1065 ASN

Total number of N/Q/H flips: 25

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.147551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.111996 restraints weight = 26659.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 2.34
r_work: 0.3054 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2906 r_free = 0.2906    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2906
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18705  Z= 0.134
  Angle     :  0.573   8.529  25284  Z= 0.298
  Chirality :  0.042   0.158   2817
  Planarity :  0.005   0.066   3153
  Dihedral  : 14.895  85.256   3011
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.07 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  6.42 %
    Allowed  : 23.12 %
    Favored  : 70.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.37 (0.17), residues: 2194
  helix: -0.24 (0.15), residues: 1085
  sheet: -2.29 (0.32), residues: 210
  loop : -3.11 (0.19), residues: 899

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP F 187 
 HIS   0.003   0.001   HIS F 888 
 PHE   0.022   0.001   PHE A1185 
 TYR   0.011   0.001   TYR F 163 
 ARG   0.005   0.000   ARG E 138 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03785 (  831)
  hydrogen bonds       : angle       4.36543 ( 2459)
  SS BOND              : bond        0.00302 (   12)
  SS BOND              : angle       1.09346 (   24)
  covalent geometry    : bond        0.00306 (18688)
  covalent geometry    : angle       0.57215 (25260)
  Misc. bond           : bond        0.00071 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  406 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 126
    poor density    : 280
  time to evaluate  : 1.971 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8510 (mtm)
REVERT: A   92 PHE cc_start: 0.8390 (t80) cc_final: 0.8132 (t80)
REVERT: A  182 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8090 (tt)
REVERT: A  307 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8599 (t0)
REVERT: A  340 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6649 (mm-30)
REVERT: A  483 MET cc_start: 0.3289 (tmm) cc_final: 0.2991 (tpt)
REVERT: A  599 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8663 (p0)
REVERT: A  828 ARG cc_start: 0.4764 (ttp-170) cc_final: 0.4083 (tpp-160)
REVERT: A  938 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7930 (mp)
REVERT: A 1059 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.7911 (mt)
REVERT: A 1060 PHE cc_start: 0.8077 (OUTLIER) cc_final: 0.7126 (t80)
REVERT: A 1186 ASP cc_start: 0.8682 (t0) cc_final: 0.8318 (t0)
REVERT: A 1205 PHE cc_start: 0.4219 (t80) cc_final: 0.3907 (t80)
REVERT: A 1286 MET cc_start: 0.8990 (mtp) cc_final: 0.8698 (mtm)
REVERT: A 1304 ASN cc_start: 0.9289 (t0) cc_final: 0.9034 (t0)
REVERT: E  189 PHE cc_start: 0.6819 (t80) cc_final: 0.6617 (t80)
REVERT: F  281 MET cc_start: 0.9095 (tpp) cc_final: 0.8791 (ttm)
REVERT: F  348 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8550 (t0)
REVERT: F  380 LYS cc_start: 0.8787 (ttpp) cc_final: 0.8246 (ttpt)
REVERT: F  442 LYS cc_start: 0.9132 (ttpp) cc_final: 0.8725 (ttpt)
REVERT: F  593 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8566 (pp)
REVERT: F  604 LYS cc_start: 0.8792 (mtmm) cc_final: 0.8366 (mttm)
REVERT: F  669 TYR cc_start: 0.8446 (m-80) cc_final: 0.8233 (m-80)
REVERT: F  727 LYS cc_start: 0.9079 (tppt) cc_final: 0.8815 (mmtt)
REVERT: F  858 ASP cc_start: 0.8622 (p0) cc_final: 0.8251 (p0)
REVERT: F 1005 ILE cc_start: 0.8649 (mt) cc_final: 0.8367 (mt)
REVERT: F 1035 ILE cc_start: 0.8683 (pt) cc_final: 0.8344 (mt)
  outliers start: 126
  outliers final: 83
  residues processed: 382
  average time/residue: 0.2755
  time to fit residues: 165.0581
Evaluate side-chains
  341 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 249
  time to evaluate  : 2.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  453 HIS
Chi-restraints excluded: chain A residue  468 ASN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  510 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  599 ASN
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  792 CYS
Chi-restraints excluded: chain A residue  804 PHE
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  938 LEU
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1052 ILE
Chi-restraints excluded: chain A residue 1059 ILE
Chi-restraints excluded: chain A residue 1060 PHE
Chi-restraints excluded: chain A residue 1069 GLN
Chi-restraints excluded: chain A residue 1108 GLN
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1343 ASP
Chi-restraints excluded: chain A residue 1400 ASP
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain E residue  162 VAL
Chi-restraints excluded: chain F residue   32 THR
Chi-restraints excluded: chain F residue   61 TYR
Chi-restraints excluded: chain F residue   74 ASN
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  181 VAL
Chi-restraints excluded: chain F residue  200 GLU
Chi-restraints excluded: chain F residue  205 LEU
Chi-restraints excluded: chain F residue  270 THR
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  348 ASN
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  401 ILE
Chi-restraints excluded: chain F residue  421 ILE
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  478 LYS
Chi-restraints excluded: chain F residue  543 LEU
Chi-restraints excluded: chain F residue  593 LEU
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  617 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  677 ASP
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  815 VAL
Chi-restraints excluded: chain F residue  817 ILE
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  850 VAL
Chi-restraints excluded: chain F residue  853 CYS
Chi-restraints excluded: chain F residue  982 THR
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1014 THR
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1027 CYS
Chi-restraints excluded: chain F residue 1038 GLU
Chi-restraints excluded: chain F residue 1062 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 221
   random chunks:
   chunk 142 optimal weight:    4.9990
   chunk 32 optimal weight:    7.9990
   chunk 201 optimal weight:    7.9990
   chunk 85 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 214 optimal weight:    1.9990
   chunk 115 optimal weight:    9.9990
   chunk 118 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 157 optimal weight:    2.9990
   chunk 171 optimal weight:    5.9990
   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  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 302 ASN
A 327 ASN
A 453 HIS
A 547 ASN
A 599 ASN
A 930 ASN
A 999 ASN
A1058 ASN
A1108 GLN
** A1383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  74 ASN
** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 888 HIS
** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.143565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.107948 restraints weight = 26840.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.30
r_work: 0.2986 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2849
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2849 r_free = 0.2849    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2849
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.088  18705  Z= 0.287
  Angle     :  0.660   9.373  25284  Z= 0.343
  Chirality :  0.046   0.210   2817
  Planarity :  0.005   0.060   3153
  Dihedral  : 14.157  85.406   2909
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  7.66 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  7.89 %
    Allowed  : 22.20 %
    Favored  : 69.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.17), residues: 2194
  helix: -0.07 (0.16), residues: 1097
  sheet: -2.10 (0.33), residues: 210
  loop : -2.85 (0.19), residues: 887

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP F 187 
 HIS   0.009   0.001   HIS A 453 
 PHE   0.023   0.002   PHE A1185 
 TYR   0.018   0.002   TYR F1071 
 ARG   0.004   0.000   ARG A 584 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04479 (  831)
  hydrogen bonds       : angle       4.48076 ( 2459)
  SS BOND              : bond        0.00485 (   12)
  SS BOND              : angle       1.51213 (   24)
  covalent geometry    : bond        0.00691 (18688)
  covalent geometry    : angle       0.65824 (25260)
  Misc. bond           : bond        0.00078 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  406 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 155
    poor density    : 251
  time to evaluate  : 1.877 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8717 (mtm)
REVERT: A  182 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8200 (tt)
REVERT: A  464 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.7066 (mt0)
REVERT: A  828 ARG cc_start: 0.4771 (ttp-170) cc_final: 0.4055 (tpp-160)
REVERT: A  938 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.7986 (mp)
REVERT: A 1018 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8444 (mt0)
REVERT: A 1029 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7572 (tp30)
REVERT: A 1060 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7158 (t80)
REVERT: A 1186 ASP cc_start: 0.8740 (t0) cc_final: 0.8277 (t0)
REVERT: A 1205 PHE cc_start: 0.4213 (t80) cc_final: 0.3864 (t80)
REVERT: E  110 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.7991 (mt)
REVERT: E  189 PHE cc_start: 0.6844 (t80) cc_final: 0.6569 (t80)
REVERT: F  114 ARG cc_start: 0.8509 (mtp85) cc_final: 0.8213 (mtt90)
REVERT: F  248 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.8902 (pp30)
REVERT: F  380 LYS cc_start: 0.8839 (ttpp) cc_final: 0.8285 (ttpt)
REVERT: F  604 LYS cc_start: 0.8832 (mtmm) cc_final: 0.8446 (mttm)
REVERT: F  727 LYS cc_start: 0.9060 (tppt) cc_final: 0.8483 (mmtt)
REVERT: F  728 ASN cc_start: 0.8362 (m-40) cc_final: 0.7803 (t0)
REVERT: F  858 ASP cc_start: 0.8673 (p0) cc_final: 0.8409 (p0)
  outliers start: 155
  outliers final: 110
  residues processed: 375
  average time/residue: 0.2807
  time to fit residues: 166.9093
Evaluate side-chains
  358 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 119
    poor density    : 239
  time to evaluate  : 1.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   56 ILE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   70 VAL
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  179 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  255 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  324 PHE
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  468 ASN
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  510 GLU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  619 VAL
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  792 CYS
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  892 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  935 THR
Chi-restraints excluded: chain A residue  938 LEU
Chi-restraints excluded: chain A residue  999 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1018 GLN
Chi-restraints excluded: chain A residue 1029 GLU
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1052 ILE
Chi-restraints excluded: chain A residue 1058 ASN
Chi-restraints excluded: chain A residue 1060 PHE
Chi-restraints excluded: chain A residue 1069 GLN
Chi-restraints excluded: chain A residue 1108 GLN
Chi-restraints excluded: chain A residue 1111 VAL
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1198 ILE
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1343 ASP
Chi-restraints excluded: chain A residue 1380 ILE
Chi-restraints excluded: chain A residue 1388 THR
Chi-restraints excluded: chain A residue 1400 ASP
Chi-restraints excluded: chain E residue   24 MET
Chi-restraints excluded: chain E residue  110 ILE
Chi-restraints excluded: chain E residue  134 ASP
Chi-restraints excluded: chain E residue  162 VAL
Chi-restraints excluded: chain F residue   32 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   61 TYR
Chi-restraints excluded: chain F residue   74 ASN
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  124 VAL
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  180 ILE
Chi-restraints excluded: chain F residue  181 VAL
Chi-restraints excluded: chain F residue  194 VAL
Chi-restraints excluded: chain F residue  200 GLU
Chi-restraints excluded: chain F residue  205 LEU
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain F residue  248 GLN
Chi-restraints excluded: chain F residue  270 THR
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  348 ASN
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  401 ILE
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  479 THR
Chi-restraints excluded: chain F residue  523 VAL
Chi-restraints excluded: chain F residue  543 LEU
Chi-restraints excluded: chain F residue  608 THR
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  617 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  677 ASP
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  806 GLN
Chi-restraints excluded: chain F residue  815 VAL
Chi-restraints excluded: chain F residue  817 ILE
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  850 VAL
Chi-restraints excluded: chain F residue  853 CYS
Chi-restraints excluded: chain F residue  982 THR
Chi-restraints excluded: chain F residue  997 LEU
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1014 THR
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1026 THR
Chi-restraints excluded: chain F residue 1027 CYS
Chi-restraints excluded: chain F residue 1038 GLU
Chi-restraints excluded: chain F residue 1062 CYS
Chi-restraints excluded: chain F residue 1068 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 221
   random chunks:
   chunk 19 optimal weight:    0.0470
   chunk 11 optimal weight:    0.9990
   chunk 51 optimal weight:    9.9990
   chunk 191 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 157 optimal weight:    4.9990
   chunk 159 optimal weight:    1.9990
   chunk 173 optimal weight:    0.8980
   chunk 160 optimal weight:    0.6980
   chunk 28 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.6880

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 327 ASN
A 547 ASN
A 999 ASN
A1108 GLN
F  74 ASN
** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1039 GLN
F1065 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.148667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.112988 restraints weight = 26606.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 2.36
r_work: 0.3068 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2938
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2938 r_free = 0.2938    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2938
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  18705  Z= 0.110
  Angle     :  0.538   9.045  25284  Z= 0.279
  Chirality :  0.041   0.157   2817
  Planarity :  0.004   0.061   3153
  Dihedral  : 13.279  82.199   2896
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.97 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 24.59 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.18), residues: 2194
  helix:  0.49 (0.16), residues: 1082
  sheet: -1.92 (0.32), residues: 217
  loop : -2.57 (0.20), residues: 895

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP F 187 
 HIS   0.003   0.000   HIS F 888 
 PHE   0.025   0.001   PHE E 182 
 TYR   0.010   0.001   TYR F 163 
 ARG   0.004   0.000   ARG F 846 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03339 (  831)
  hydrogen bonds       : angle       4.05554 ( 2459)
  SS BOND              : bond        0.00411 (   12)
  SS BOND              : angle       2.08419 (   24)
  covalent geometry    : bond        0.00243 (18688)
  covalent geometry    : angle       0.53424 (25260)
  Misc. bond           : bond        0.00035 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 111
    poor density    : 274
  time to evaluate  : 1.811 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8008 (tt)
REVERT: A  183 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7516 (mt0)
REVERT: A  483 MET cc_start: 0.3194 (tmm) cc_final: 0.2851 (tpt)
REVERT: A  828 ARG cc_start: 0.4621 (ttp-170) cc_final: 0.4025 (tpp-160)
REVERT: A  916 HIS cc_start: 0.4216 (t-90) cc_final: 0.2347 (m90)
REVERT: A 1060 PHE cc_start: 0.7987 (OUTLIER) cc_final: 0.7063 (t80)
REVERT: A 1108 GLN cc_start: 0.5905 (OUTLIER) cc_final: 0.5648 (pp30)
REVERT: A 1186 ASP cc_start: 0.8554 (t0) cc_final: 0.8020 (t0)
REVERT: A 1205 PHE cc_start: 0.4109 (t80) cc_final: 0.3833 (t80)
REVERT: A 1286 MET cc_start: 0.8975 (mtp) cc_final: 0.8684 (mtm)
REVERT: E  206 ARG cc_start: 0.6015 (OUTLIER) cc_final: 0.5257 (mmp-170)
REVERT: F  114 ARG cc_start: 0.8317 (mtp85) cc_final: 0.7927 (mtt180)
REVERT: F  248 GLN cc_start: 0.9313 (OUTLIER) cc_final: 0.8878 (pp30)
REVERT: F  281 MET cc_start: 0.9097 (tpp) cc_final: 0.8792 (ttm)
REVERT: F  380 LYS cc_start: 0.8866 (ttpp) cc_final: 0.8357 (ttpt)
REVERT: F  442 LYS cc_start: 0.9006 (ttpp) cc_final: 0.8769 (ttpt)
REVERT: F  604 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8329 (mttm)
REVERT: F  669 TYR cc_start: 0.8070 (m-80) cc_final: 0.7850 (m-80)
REVERT: F  727 LYS cc_start: 0.8984 (tppt) cc_final: 0.8524 (mmtt)
REVERT: F  728 ASN cc_start: 0.8364 (m-40) cc_final: 0.7641 (t0)
REVERT: F  858 ASP cc_start: 0.8631 (p0) cc_final: 0.8262 (p0)
  outliers start: 111
  outliers final: 81
  residues processed: 356
  average time/residue: 0.2750
  time to fit residues: 153.1205
Evaluate side-chains
  342 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 255
  time to evaluate  : 1.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  468 ASN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  792 CYS
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  925 ILE
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  999 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1060 PHE
Chi-restraints excluded: chain A residue 1069 GLN
Chi-restraints excluded: chain A residue 1108 GLN
Chi-restraints excluded: chain A residue 1111 VAL
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1343 ASP
Chi-restraints excluded: chain A residue 1388 THR
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1400 ASP
Chi-restraints excluded: chain E residue   24 MET
Chi-restraints excluded: chain E residue  206 ARG
Chi-restraints excluded: chain F residue   32 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   61 TYR
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  160 GLN
Chi-restraints excluded: chain F residue  181 VAL
Chi-restraints excluded: chain F residue  205 LEU
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain F residue  248 GLN
Chi-restraints excluded: chain F residue  270 THR
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  401 ILE
Chi-restraints excluded: chain F residue  421 ILE
Chi-restraints excluded: chain F residue  543 LEU
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  617 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  677 ASP
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  817 ILE
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  982 THR
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1014 THR
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1027 CYS
Chi-restraints excluded: chain F residue 1038 GLU
Chi-restraints excluded: chain F residue 1062 CYS
Chi-restraints excluded: chain F residue 1068 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 221
   random chunks:
   chunk 107 optimal weight:    9.9990
   chunk 155 optimal weight:    0.7980
   chunk 110 optimal weight:    8.9990
   chunk 213 optimal weight:   10.0000
   chunk 180 optimal weight:    0.9990
   chunk 70 optimal weight:    0.0870
   chunk 18 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 170 optimal weight:    3.9990
   chunk 105 optimal weight:    1.9990
   chunk 157 optimal weight:    2.9990
   overall best weight:    0.9562

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 999 ASN
A1108 GLN
** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1065 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.148401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.113193 restraints weight = 26757.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.32
r_work: 0.3068 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2932 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2932
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2934
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2934 r_free = 0.2934    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2934
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18705  Z= 0.117
  Angle     :  0.534   8.471  25284  Z= 0.276
  Chirality :  0.041   0.166   2817
  Planarity :  0.004   0.058   3153
  Dihedral  : 12.669  81.007   2880
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.11 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 24.75 %
    Favored  : 68.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.18), residues: 2194
  helix:  0.68 (0.16), residues: 1095
  sheet: -1.74 (0.33), residues: 210
  loop : -2.37 (0.20), residues: 889

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP F 187 
 HIS   0.002   0.000   HIS F 888 
 PHE   0.028   0.001   PHE A  92 
 TYR   0.024   0.001   TYR A1101 
 ARG   0.006   0.000   ARG F 846 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  831)
  hydrogen bonds       : angle       3.95969 ( 2459)
  SS BOND              : bond        0.00269 (   12)
  SS BOND              : angle       1.80264 (   24)
  covalent geometry    : bond        0.00269 (18688)
  covalent geometry    : angle       0.53163 (25260)
  Misc. bond           : bond        0.00060 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 124
    poor density    : 279
  time to evaluate  : 2.037 
Fit side-chains
REVERT: A   74 MET cc_start: 0.9164 (OUTLIER) cc_final: 0.8540 (mtm)
REVERT: A  182 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7967 (tt)
REVERT: A  183 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7485 (mt0)
REVERT: A  464 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7053 (mt0)
REVERT: A  483 MET cc_start: 0.3090 (tmm) cc_final: 0.2712 (tpt)
REVERT: A  828 ARG cc_start: 0.4655 (ttp-170) cc_final: 0.4082 (tpp-160)
REVERT: A 1018 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8335 (mt0)
REVERT: A 1060 PHE cc_start: 0.8134 (OUTLIER) cc_final: 0.7202 (t80)
REVERT: A 1186 ASP cc_start: 0.8511 (t0) cc_final: 0.8049 (t0)
REVERT: A 1239 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7698 (ptp-170)
REVERT: E  206 ARG cc_start: 0.6047 (OUTLIER) cc_final: 0.5225 (mmp-170)
REVERT: F  114 ARG cc_start: 0.8334 (mtp85) cc_final: 0.7896 (mtt180)
REVERT: F  281 MET cc_start: 0.9108 (tpp) cc_final: 0.8773 (ttm)
REVERT: F  380 LYS cc_start: 0.8889 (ttpp) cc_final: 0.8361 (ttpt)
REVERT: F  442 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8690 (ttpt)
REVERT: F  727 LYS cc_start: 0.8993 (tppt) cc_final: 0.8531 (mmtt)
REVERT: F  728 ASN cc_start: 0.8348 (m-40) cc_final: 0.7682 (t0)
REVERT: F  858 ASP cc_start: 0.8629 (p0) cc_final: 0.8258 (p0)
  outliers start: 124
  outliers final: 89
  residues processed: 373
  average time/residue: 0.2722
  time to fit residues: 159.8668
Evaluate side-chains
  355 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 97
    poor density    : 258
  time to evaluate  : 2.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  792 CYS
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  999 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1018 GLN
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1060 PHE
Chi-restraints excluded: chain A residue 1108 GLN
Chi-restraints excluded: chain A residue 1111 VAL
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1198 ILE
Chi-restraints excluded: chain A residue 1239 ARG
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1343 ASP
Chi-restraints excluded: chain A residue 1380 ILE
Chi-restraints excluded: chain A residue 1381 MET
Chi-restraints excluded: chain A residue 1388 THR
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1400 ASP
Chi-restraints excluded: chain A residue 1429 ILE
Chi-restraints excluded: chain E residue   24 MET
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain E residue  206 ARG
Chi-restraints excluded: chain F residue   32 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   61 TYR
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  194 VAL
Chi-restraints excluded: chain F residue  205 LEU
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain F residue  248 GLN
Chi-restraints excluded: chain F residue  270 THR
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  401 ILE
Chi-restraints excluded: chain F residue  421 ILE
Chi-restraints excluded: chain F residue  476 GLU
Chi-restraints excluded: chain F residue  543 LEU
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  617 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  716 ASN
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  815 VAL
Chi-restraints excluded: chain F residue  817 ILE
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  850 VAL
Chi-restraints excluded: chain F residue  853 CYS
Chi-restraints excluded: chain F residue  982 THR
Chi-restraints excluded: chain F residue  997 LEU
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1014 THR
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1027 CYS
Chi-restraints excluded: chain F residue 1038 GLU
Chi-restraints excluded: chain F residue 1062 CYS
Chi-restraints excluded: chain F residue 1068 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 221
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 189 optimal weight:    1.9990
   chunk 129 optimal weight:    0.7980
   chunk 62 optimal weight:    9.9990
   chunk 25 optimal weight:    1.9990
   chunk 104 optimal weight:    4.9990
   chunk 162 optimal weight:    0.0670
   chunk 66 optimal weight:    0.9990
   chunk 194 optimal weight:    2.9990
   chunk 26 optimal weight:    0.8980
   chunk 171 optimal weight:    2.9990
   overall best weight:    0.9522

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 999 ASN
A1108 GLN
A1398 HIS
** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1065 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.149231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.113225 restraints weight = 26883.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.33
r_work: 0.3075 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2940 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2940
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2943
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2943 r_free = 0.2943    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2943
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18705  Z= 0.117
  Angle     :  0.535   9.225  25284  Z= 0.276
  Chirality :  0.041   0.157   2817
  Planarity :  0.004   0.059   3153
  Dihedral  : 12.264  80.640   2872
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.84 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 25.00 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.18), residues: 2194
  helix:  0.85 (0.16), residues: 1095
  sheet: -1.64 (0.33), residues: 210
  loop : -2.25 (0.20), residues: 889

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP F 187 
 HIS   0.002   0.000   HIS F 888 
 PHE   0.024   0.001   PHE A  92 
 TYR   0.027   0.001   TYR A1101 
 ARG   0.012   0.000   ARG A1099 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03211 (  831)
  hydrogen bonds       : angle       3.90186 ( 2459)
  SS BOND              : bond        0.00274 (   12)
  SS BOND              : angle       1.60768 (   24)
  covalent geometry    : bond        0.00271 (18688)
  covalent geometry    : angle       0.53263 (25260)
  Misc. bond           : bond        0.00048 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  386 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 124
    poor density    : 262
  time to evaluate  : 2.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8544 (mtm)
REVERT: A  182 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7962 (tt)
REVERT: A  183 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7460 (mt0)
REVERT: A  464 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7027 (mt0)
REVERT: A  483 MET cc_start: 0.3260 (tmm) cc_final: 0.2745 (tpt)
REVERT: A  500 ASP cc_start: 0.7360 (OUTLIER) cc_final: 0.6901 (p0)
REVERT: A  828 ARG cc_start: 0.4721 (ttp-170) cc_final: 0.4105 (tpp-160)
REVERT: A 1018 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8319 (mt0)
REVERT: A 1058 ASN cc_start: 0.7753 (m-40) cc_final: 0.7490 (t0)
REVERT: A 1060 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7258 (t80)
REVERT: A 1163 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8140 (tp)
REVERT: A 1186 ASP cc_start: 0.8522 (t0) cc_final: 0.8078 (t0)
REVERT: A 1239 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7704 (ptp-170)
REVERT: A 1286 MET cc_start: 0.8941 (mtp) cc_final: 0.8638 (mtm)
REVERT: E  206 ARG cc_start: 0.5964 (OUTLIER) cc_final: 0.5096 (mmp-170)
REVERT: F  281 MET cc_start: 0.9117 (tpp) cc_final: 0.8755 (ttm)
REVERT: F  380 LYS cc_start: 0.8887 (ttpp) cc_final: 0.8394 (ttpt)
REVERT: F  442 LYS cc_start: 0.8954 (ttpp) cc_final: 0.8671 (ttpt)
REVERT: F  604 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8311 (mttm)
REVERT: F  727 LYS cc_start: 0.8998 (tppt) cc_final: 0.8538 (mmtt)
REVERT: F  728 ASN cc_start: 0.8345 (m-40) cc_final: 0.7691 (t0)
REVERT: F  858 ASP cc_start: 0.8594 (p0) cc_final: 0.8249 (p0)
  outliers start: 124
  outliers final: 95
  residues processed: 358
  average time/residue: 0.2843
  time to fit residues: 159.1889
Evaluate side-chains
  362 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 105
    poor density    : 257
  time to evaluate  : 1.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue   74 MET
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  273 THR
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  468 ASN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  999 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1018 GLN
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1060 PHE
Chi-restraints excluded: chain A residue 1108 GLN
Chi-restraints excluded: chain A residue 1111 VAL
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1198 ILE
Chi-restraints excluded: chain A residue 1205 PHE
Chi-restraints excluded: chain A residue 1239 ARG
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1343 ASP
Chi-restraints excluded: chain A residue 1381 MET
Chi-restraints excluded: chain A residue 1388 THR
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1400 ASP
Chi-restraints excluded: chain A residue 1429 ILE
Chi-restraints excluded: chain E residue   24 MET
Chi-restraints excluded: chain E residue  153 VAL
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain E residue  206 ARG
Chi-restraints excluded: chain F residue   32 THR
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   61 TYR
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  181 VAL
Chi-restraints excluded: chain F residue  194 VAL
Chi-restraints excluded: chain F residue  205 LEU
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain F residue  248 GLN
Chi-restraints excluded: chain F residue  270 THR
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  401 ILE
Chi-restraints excluded: chain F residue  421 ILE
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  543 LEU
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  617 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  716 ASN
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  817 ILE
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  850 VAL
Chi-restraints excluded: chain F residue  853 CYS
Chi-restraints excluded: chain F residue  982 THR
Chi-restraints excluded: chain F residue  997 LEU
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1014 THR
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1026 THR
Chi-restraints excluded: chain F residue 1027 CYS
Chi-restraints excluded: chain F residue 1038 GLU
Chi-restraints excluded: chain F residue 1062 CYS
Chi-restraints excluded: chain F residue 1068 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 221
   random chunks:
   chunk 58 optimal weight:    7.9990
   chunk 53 optimal weight:   40.0000
   chunk 217 optimal weight:    5.9990
   chunk 127 optimal weight:    0.5980
   chunk 172 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    0.4980
   chunk 17 optimal weight:    5.9990
   chunk 116 optimal weight:    0.5980
   chunk 185 optimal weight:    5.9990
   chunk 166 optimal weight:    0.0030
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 999 ASN
** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1065 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.151349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.115452 restraints weight = 26576.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3339 rms_B_bonded: 2.32
r_work: 0.3110 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2978
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2978 r_free = 0.2978    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2978
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  18705  Z= 0.100
  Angle     :  0.519   9.702  25284  Z= 0.267
  Chirality :  0.040   0.150   2817
  Planarity :  0.004   0.058   3153
  Dihedral  : 11.795  80.353   2871
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.61 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  5.45 %
    Allowed  : 25.56 %
    Favored  : 68.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.18), residues: 2194
  helix:  0.93 (0.16), residues: 1110
  sheet: -1.57 (0.33), residues: 210
  loop : -2.17 (0.21), residues: 874

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP F 187 
 HIS   0.002   0.000   HIS A1398 
 PHE   0.021   0.001   PHE A  92 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.009   0.000   ARG F 846 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02924 (  831)
  hydrogen bonds       : angle       3.79547 ( 2459)
  SS BOND              : bond        0.00219 (   12)
  SS BOND              : angle       1.41032 (   24)
  covalent geometry    : bond        0.00222 (18688)
  covalent geometry    : angle       0.51765 (25260)
  Misc. bond           : bond        0.00028 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 107
    poor density    : 290
  time to evaluate  : 1.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7941 (tt)
REVERT: A  183 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.7446 (mt0)
REVERT: A  243 SER cc_start: 0.9284 (p) cc_final: 0.9084 (t)
REVERT: A  326 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8376 (mp)
REVERT: A  460 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8476 (tp)
REVERT: A  464 GLN cc_start: 0.7616 (OUTLIER) cc_final: 0.7182 (mt0)
REVERT: A  480 LEU cc_start: 0.3349 (OUTLIER) cc_final: 0.3103 (mp)
REVERT: A  483 MET cc_start: 0.3266 (tmm) cc_final: 0.2860 (tpt)
REVERT: A  500 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6845 (p0)
REVERT: A  527 LEU cc_start: 0.8388 (mm) cc_final: 0.8173 (mm)
REVERT: A  828 ARG cc_start: 0.4666 (ttp-170) cc_final: 0.4095 (tpp-160)
REVERT: A  916 HIS cc_start: 0.3632 (t-90) cc_final: 0.1791 (m90)
REVERT: A 1018 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8281 (mt0)
REVERT: A 1058 ASN cc_start: 0.7726 (m-40) cc_final: 0.7524 (t0)
REVERT: A 1163 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8109 (tp)
REVERT: A 1182 TRP cc_start: 0.8896 (m100) cc_final: 0.8687 (m100)
REVERT: A 1186 ASP cc_start: 0.8408 (t0) cc_final: 0.8010 (t0)
REVERT: E   30 ASP cc_start: 0.6121 (m-30) cc_final: 0.5824 (m-30)
REVERT: E  206 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.5127 (mmp-170)
REVERT: F  281 MET cc_start: 0.9050 (tpp) cc_final: 0.8729 (ttm)
REVERT: F  311 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8840 (tp40)
REVERT: F  380 LYS cc_start: 0.8884 (ttpp) cc_final: 0.8332 (ttpt)
REVERT: F  593 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8565 (pp)
REVERT: F  727 LYS cc_start: 0.8974 (tppt) cc_final: 0.8691 (mmtm)
REVERT: F  728 ASN cc_start: 0.8385 (m-40) cc_final: 0.7749 (t0)
REVERT: F  858 ASP cc_start: 0.8544 (p0) cc_final: 0.8188 (p0)
  outliers start: 107
  outliers final: 76
  residues processed: 372
  average time/residue: 0.2658
  time to fit residues: 155.5514
Evaluate side-chains
  351 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 263
  time to evaluate  : 1.789 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  541 TYR
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  925 ILE
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  999 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1018 GLN
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1111 VAL
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1343 ASP
Chi-restraints excluded: chain A residue 1381 MET
Chi-restraints excluded: chain A residue 1388 THR
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1400 ASP
Chi-restraints excluded: chain A residue 1429 ILE
Chi-restraints excluded: chain E residue  153 VAL
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain E residue  206 ARG
Chi-restraints excluded: chain F residue   32 THR
Chi-restraints excluded: chain F residue   61 TYR
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  181 VAL
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain F residue  248 GLN
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  311 GLN
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  401 ILE
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  543 LEU
Chi-restraints excluded: chain F residue  593 LEU
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  617 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  817 ILE
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  850 VAL
Chi-restraints excluded: chain F residue  853 CYS
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1027 CYS
Chi-restraints excluded: chain F residue 1038 GLU
Chi-restraints excluded: chain F residue 1068 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 221
   random chunks:
   chunk 198 optimal weight:    1.9990
   chunk 152 optimal weight:    1.9990
   chunk 153 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 186 optimal weight:    5.9990
   chunk 94 optimal weight:    0.4980
   chunk 33 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 159 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 164 optimal weight:    3.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 999 ASN
A1108 GLN
A1154 ASN
A1383 ASN
** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 551 GLN
** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1065 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.149020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.114530 restraints weight = 26783.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 2.43
r_work: 0.3062 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2926 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2926
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2929
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2929 r_free = 0.2929    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2929
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  18705  Z= 0.140
  Angle     :  0.544   7.721  25284  Z= 0.282
  Chirality :  0.042   0.157   2817
  Planarity :  0.004   0.058   3153
  Dihedral  : 11.662  81.931   2863
  Min Nonbonded Distance : 2.268

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.11 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 25.81 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.18), residues: 2194
  helix:  0.98 (0.16), residues: 1101
  sheet: -1.59 (0.32), residues: 213
  loop : -2.11 (0.21), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP F 187 
 HIS   0.002   0.001   HIS A1398 
 PHE   0.020   0.001   PHE A  92 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.008   0.000   ARG F 846 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03225 (  831)
  hydrogen bonds       : angle       3.83704 ( 2459)
  SS BOND              : bond        0.00260 (   12)
  SS BOND              : angle       1.49074 (   24)
  covalent geometry    : bond        0.00335 (18688)
  covalent geometry    : angle       0.54237 (25260)
  Misc. bond           : bond        0.00045 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  378 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 110
    poor density    : 268
  time to evaluate  : 2.072 
Fit side-chains
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8005 (tt)
REVERT: A  183 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7451 (mt0)
REVERT: A  326 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8395 (mp)
REVERT: A  464 GLN cc_start: 0.7589 (OUTLIER) cc_final: 0.7115 (mt0)
REVERT: A  480 LEU cc_start: 0.3395 (OUTLIER) cc_final: 0.3114 (mp)
REVERT: A  483 MET cc_start: 0.3200 (tmm) cc_final: 0.2739 (tpt)
REVERT: A  500 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6848 (p0)
REVERT: A  828 ARG cc_start: 0.4447 (ttp-170) cc_final: 0.3873 (tpp-160)
REVERT: A  916 HIS cc_start: 0.3775 (t-90) cc_final: 0.1828 (m90)
REVERT: A 1018 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8307 (mt0)
REVERT: A 1163 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8100 (tp)
REVERT: A 1182 TRP cc_start: 0.8874 (m100) cc_final: 0.8631 (m100)
REVERT: A 1186 ASP cc_start: 0.8433 (t0) cc_final: 0.8068 (t0)
REVERT: E   30 ASP cc_start: 0.6052 (m-30) cc_final: 0.5835 (m-30)
REVERT: E  206 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.5332 (mmp-170)
REVERT: F  114 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7992 (mtt90)
REVERT: F  281 MET cc_start: 0.9171 (tpp) cc_final: 0.8410 (tpp)
REVERT: F  311 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8759 (tp40)
REVERT: F  380 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8168 (ttpt)
REVERT: F  593 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8654 (pp)
REVERT: F  727 LYS cc_start: 0.9014 (tppt) cc_final: 0.8566 (mmtt)
REVERT: F  728 ASN cc_start: 0.8406 (m-40) cc_final: 0.7840 (t0)
REVERT: F  858 ASP cc_start: 0.8624 (p0) cc_final: 0.8290 (p0)
  outliers start: 110
  outliers final: 88
  residues processed: 354
  average time/residue: 0.2692
  time to fit residues: 150.7945
Evaluate side-chains
  355 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 99
    poor density    : 256
  time to evaluate  : 1.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  468 ASN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  999 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1018 GLN
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1108 GLN
Chi-restraints excluded: chain A residue 1111 VAL
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1198 ILE
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1343 ASP
Chi-restraints excluded: chain A residue 1380 ILE
Chi-restraints excluded: chain A residue 1381 MET
Chi-restraints excluded: chain A residue 1388 THR
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1400 ASP
Chi-restraints excluded: chain A residue 1429 ILE
Chi-restraints excluded: chain E residue  153 VAL
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain E residue  206 ARG
Chi-restraints excluded: chain F residue   32 THR
Chi-restraints excluded: chain F residue   36 TRP
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   61 TYR
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  181 VAL
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain F residue  248 GLN
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  311 GLN
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  401 ILE
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  543 LEU
Chi-restraints excluded: chain F residue  593 LEU
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  617 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  716 ASN
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  817 ILE
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  850 VAL
Chi-restraints excluded: chain F residue  853 CYS
Chi-restraints excluded: chain F residue  982 THR
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1026 THR
Chi-restraints excluded: chain F residue 1027 CYS
Chi-restraints excluded: chain F residue 1038 GLU
Chi-restraints excluded: chain F residue 1068 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 221
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 111 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 153 optimal weight:    0.9990
   chunk 172 optimal weight:    0.7980
   chunk 87 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 162 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 130 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   overall best weight:    1.0786

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 999 ASN
A1108 GLN
** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1065 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.149256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.113539 restraints weight = 26762.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.29
r_work: 0.3078 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2947
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2947 r_free = 0.2947    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2947
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  18705  Z= 0.123
  Angle     :  0.540   7.759  25284  Z= 0.279
  Chirality :  0.041   0.205   2817
  Planarity :  0.004   0.057   3153
  Dihedral  : 11.521  81.805   2863
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.70 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  5.30 %
    Allowed  : 26.27 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.18), residues: 2194
  helix:  1.02 (0.16), residues: 1098
  sheet: -1.60 (0.32), residues: 215
  loop : -2.06 (0.21), residues: 881

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP F 187 
 HIS   0.002   0.000   HIS A1398 
 PHE   0.023   0.001   PHE A1055 
 TYR   0.014   0.001   TYR F 632 
 ARG   0.007   0.000   ARG F 846 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03163 (  831)
  hydrogen bonds       : angle       3.80915 ( 2459)
  SS BOND              : bond        0.00246 (   12)
  SS BOND              : angle       1.42372 (   24)
  covalent geometry    : bond        0.00289 (18688)
  covalent geometry    : angle       0.53879 (25260)
  Misc. bond           : bond        0.00035 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  361 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 104
    poor density    : 257
  time to evaluate  : 2.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8000 (tt)
REVERT: A  183 GLN cc_start: 0.8328 (OUTLIER) cc_final: 0.7521 (mt0)
REVERT: A  326 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8405 (mp)
REVERT: A  464 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7135 (mt0)
REVERT: A  480 LEU cc_start: 0.3430 (OUTLIER) cc_final: 0.3146 (mp)
REVERT: A  483 MET cc_start: 0.3203 (tmm) cc_final: 0.2737 (tpt)
REVERT: A  500 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.6779 (p0)
REVERT: A  828 ARG cc_start: 0.4415 (ttp-170) cc_final: 0.3873 (tpp-160)
REVERT: A  916 HIS cc_start: 0.3795 (t-90) cc_final: 0.1844 (m90)
REVERT: A 1018 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8314 (mt0)
REVERT: A 1163 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8097 (tp)
REVERT: A 1182 TRP cc_start: 0.8892 (m100) cc_final: 0.8660 (m100)
REVERT: A 1186 ASP cc_start: 0.8410 (t0) cc_final: 0.8012 (t0)
REVERT: A 1286 MET cc_start: 0.9059 (mtp) cc_final: 0.8855 (mtm)
REVERT: E  206 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5370 (mmp-170)
REVERT: F  281 MET cc_start: 0.9140 (tpp) cc_final: 0.8367 (tpp)
REVERT: F  311 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8787 (tp40)
REVERT: F  380 LYS cc_start: 0.8872 (ttpp) cc_final: 0.8387 (ttpt)
REVERT: F  593 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8611 (pp)
REVERT: F  727 LYS cc_start: 0.8989 (tppt) cc_final: 0.8553 (mmtt)
REVERT: F  728 ASN cc_start: 0.8365 (m-40) cc_final: 0.7855 (t0)
REVERT: F  772 ASP cc_start: 0.8153 (m-30) cc_final: 0.7788 (m-30)
REVERT: F  858 ASP cc_start: 0.8599 (p0) cc_final: 0.8240 (p0)
REVERT: F 1049 MET cc_start: 0.8295 (ttm) cc_final: 0.7941 (mtp)
  outliers start: 104
  outliers final: 86
  residues processed: 338
  average time/residue: 0.2778
  time to fit residues: 148.3347
Evaluate side-chains
  352 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 97
    poor density    : 255
  time to evaluate  : 2.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  291 MET
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  433 VAL
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  468 ASN
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  999 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1018 GLN
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1108 GLN
Chi-restraints excluded: chain A residue 1111 VAL
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1343 ASP
Chi-restraints excluded: chain A residue 1381 MET
Chi-restraints excluded: chain A residue 1388 THR
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1400 ASP
Chi-restraints excluded: chain A residue 1429 ILE
Chi-restraints excluded: chain E residue  153 VAL
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain E residue  206 ARG
Chi-restraints excluded: chain F residue   32 THR
Chi-restraints excluded: chain F residue   36 TRP
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   61 TYR
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  181 VAL
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain F residue  248 GLN
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  311 GLN
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  401 ILE
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  543 LEU
Chi-restraints excluded: chain F residue  593 LEU
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  617 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  716 ASN
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  817 ILE
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  850 VAL
Chi-restraints excluded: chain F residue  853 CYS
Chi-restraints excluded: chain F residue  982 THR
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1026 THR
Chi-restraints excluded: chain F residue 1027 CYS
Chi-restraints excluded: chain F residue 1038 GLU
Chi-restraints excluded: chain F residue 1062 CYS
Chi-restraints excluded: chain F residue 1068 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 221
   random chunks:
   chunk 170 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 103 optimal weight:    9.9990
   chunk 7 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0870
   chunk 49 optimal weight:    0.1980
   chunk 171 optimal weight:    0.9980
   chunk 110 optimal weight:    0.0470
   chunk 124 optimal weight:    2.9990
   chunk 187 optimal weight:    4.9990
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
** A  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN
A 999 ASN
A1108 GLN
** A1397 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F1007 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F1065 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.150762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.115486 restraints weight = 26724.498|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 2.28
r_work: 0.3103 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2975 r_free = 0.2975    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  18705  Z= 0.107
  Angle     :  0.534   7.395  25284  Z= 0.275
  Chirality :  0.041   0.158   2817
  Planarity :  0.004   0.057   3153
  Dihedral  : 11.319  81.513   2863
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.34 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 26.68 %
    Favored  : 68.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.30 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.18), residues: 2194
  helix:  1.12 (0.16), residues: 1096
  sheet: -1.57 (0.32), residues: 210
  loop : -1.99 (0.21), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP F 187 
 HIS   0.002   0.000   HIS A1398 
 PHE   0.021   0.001   PHE E 152 
 TYR   0.025   0.001   TYR F 632 
 ARG   0.011   0.000   ARG F 846 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03033 (  831)
  hydrogen bonds       : angle       3.76165 ( 2459)
  SS BOND              : bond        0.00225 (   12)
  SS BOND              : angle       1.30715 (   24)
  covalent geometry    : bond        0.00245 (18688)
  covalent geometry    : angle       0.53315 (25260)
  Misc. bond           : bond        0.00026 (    5)

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

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

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4388 Ramachandran restraints generated.
    2194 Oldfield, 0 Emsley, 2194 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  371 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 275
  time to evaluate  : 2.027 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7989 (tt)
REVERT: A  183 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7488 (mt0)
REVERT: A  326 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8361 (mp)
REVERT: A  464 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7053 (mt0)
REVERT: A  480 LEU cc_start: 0.3401 (OUTLIER) cc_final: 0.3108 (mp)
REVERT: A  483 MET cc_start: 0.3212 (tmm) cc_final: 0.2787 (tpt)
REVERT: A  500 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6759 (p0)
REVERT: A  828 ARG cc_start: 0.4366 (ttp-170) cc_final: 0.3778 (tpp-160)
REVERT: A  916 HIS cc_start: 0.3758 (t-90) cc_final: 0.1828 (m90)
REVERT: A 1018 GLN cc_start: 0.8827 (OUTLIER) cc_final: 0.8239 (mt0)
REVERT: A 1163 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8036 (tp)
REVERT: A 1182 TRP cc_start: 0.8844 (m100) cc_final: 0.8586 (m100)
REVERT: A 1286 MET cc_start: 0.8969 (mtp) cc_final: 0.8766 (mtm)
REVERT: E   24 MET cc_start: 0.7271 (tpp) cc_final: 0.7040 (tpp)
REVERT: E  176 TYR cc_start: 0.5424 (p90) cc_final: 0.5197 (m-10)
REVERT: E  206 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5319 (mmp-170)
REVERT: F  281 MET cc_start: 0.9111 (tpp) cc_final: 0.8738 (ttm)
REVERT: F  311 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8801 (tp40)
REVERT: F  380 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8255 (ttpt)
REVERT: F  727 LYS cc_start: 0.8983 (tppt) cc_final: 0.8694 (mmtm)
REVERT: F  728 ASN cc_start: 0.8394 (m-40) cc_final: 0.7931 (t0)
REVERT: F  858 ASP cc_start: 0.8572 (p0) cc_final: 0.8209 (p0)
REVERT: F 1049 MET cc_start: 0.8220 (ttm) cc_final: 0.7827 (mtp)
  outliers start: 96
  outliers final: 79
  residues processed: 348
  average time/residue: 0.2760
  time to fit residues: 151.8216
Evaluate side-chains
  351 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 262
  time to evaluate  : 2.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 LEU
Chi-restraints excluded: chain A residue   61 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  176 VAL
Chi-restraints excluded: chain A residue  182 LEU
Chi-restraints excluded: chain A residue  183 GLN
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  325 ILE
Chi-restraints excluded: chain A residue  326 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  439 ILE
Chi-restraints excluded: chain A residue  449 ILE
Chi-restraints excluded: chain A residue  464 GLN
Chi-restraints excluded: chain A residue  468 ASN
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  480 LEU
Chi-restraints excluded: chain A residue  500 ASP
Chi-restraints excluded: chain A residue  527 LEU
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  647 CYS
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  874 LEU
Chi-restraints excluded: chain A residue  876 VAL
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  933 LEU
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue  999 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1018 GLN
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1111 VAL
Chi-restraints excluded: chain A residue 1115 VAL
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1141 HIS
Chi-restraints excluded: chain A residue 1149 ILE
Chi-restraints excluded: chain A residue 1163 LEU
Chi-restraints excluded: chain A residue 1240 VAL
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1273 LEU
Chi-restraints excluded: chain A residue 1289 PHE
Chi-restraints excluded: chain A residue 1295 VAL
Chi-restraints excluded: chain A residue 1343 ASP
Chi-restraints excluded: chain A residue 1381 MET
Chi-restraints excluded: chain A residue 1388 THR
Chi-restraints excluded: chain A residue 1397 HIS
Chi-restraints excluded: chain A residue 1400 ASP
Chi-restraints excluded: chain A residue 1429 ILE
Chi-restraints excluded: chain E residue  153 VAL
Chi-restraints excluded: chain E residue  179 SER
Chi-restraints excluded: chain E residue  206 ARG
Chi-restraints excluded: chain F residue   36 TRP
Chi-restraints excluded: chain F residue   37 VAL
Chi-restraints excluded: chain F residue   61 TYR
Chi-restraints excluded: chain F residue  116 ASP
Chi-restraints excluded: chain F residue  125 VAL
Chi-restraints excluded: chain F residue  181 VAL
Chi-restraints excluded: chain F residue  240 VAL
Chi-restraints excluded: chain F residue  248 GLN
Chi-restraints excluded: chain F residue  303 VAL
Chi-restraints excluded: chain F residue  311 GLN
Chi-restraints excluded: chain F residue  360 ILE
Chi-restraints excluded: chain F residue  401 ILE
Chi-restraints excluded: chain F residue  423 ILE
Chi-restraints excluded: chain F residue  543 LEU
Chi-restraints excluded: chain F residue  610 THR
Chi-restraints excluded: chain F residue  612 THR
Chi-restraints excluded: chain F residue  617 THR
Chi-restraints excluded: chain F residue  652 LYS
Chi-restraints excluded: chain F residue  680 THR
Chi-restraints excluded: chain F residue  694 THR
Chi-restraints excluded: chain F residue  735 ARG
Chi-restraints excluded: chain F residue  739 THR
Chi-restraints excluded: chain F residue  744 THR
Chi-restraints excluded: chain F residue  821 VAL
Chi-restraints excluded: chain F residue  850 VAL
Chi-restraints excluded: chain F residue  853 CYS
Chi-restraints excluded: chain F residue  982 THR
Chi-restraints excluded: chain F residue 1002 CYS
Chi-restraints excluded: chain F residue 1008 VAL
Chi-restraints excluded: chain F residue 1019 ILE
Chi-restraints excluded: chain F residue 1027 CYS
Chi-restraints excluded: chain F residue 1038 GLU
Chi-restraints excluded: chain F residue 1062 CYS
Chi-restraints excluded: chain F residue 1068 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 70.6767 > 50:
  distance: 80 - 108:  32.374
  distance: 86 - 91:  13.503
  distance: 87 - 116:  31.117
  distance: 91 - 92:  12.431
  distance: 92 - 93:  26.689
  distance: 92 - 95:  12.943
  distance: 93 - 94:  33.933
  distance: 93 - 100:  23.588
  distance: 95 - 96:  25.077
  distance: 96 - 97:  17.158
  distance: 97 - 98:  28.348
  distance: 97 - 99:   3.821
  distance: 100 - 101:  18.350
  distance: 101 - 102:  22.665
  distance: 101 - 104:   4.986
  distance: 102 - 103:  33.228
  distance: 102 - 108:  28.281
  distance: 103 - 139:  29.776
  distance: 104 - 105:  26.785
  distance: 105 - 106:  26.512
  distance: 105 - 107:  26.167
  distance: 108 - 109:  12.004
  distance: 109 - 110:  33.069
  distance: 109 - 112:   8.265
  distance: 110 - 111:   9.289
  distance: 110 - 116:  23.206
  distance: 111 - 144:  24.971
  distance: 112 - 113:   7.633
  distance: 113 - 114:  18.297
  distance: 113 - 115:  25.007
  distance: 116 - 117:  30.434
  distance: 117 - 118:  60.165
  distance: 117 - 120:  11.312
  distance: 118 - 119:  12.425
  distance: 118 - 128:  68.784
  distance: 121 - 122:  18.126
  distance: 121 - 123:  17.598
  distance: 122 - 124:  15.065
  distance: 123 - 125:  41.765
  distance: 124 - 126:  17.366
  distance: 125 - 126:  40.481
  distance: 126 - 127:  41.073
  distance: 128 - 129:  22.224
  distance: 129 - 130:  35.996
  distance: 129 - 132:  21.688
  distance: 130 - 131:  12.530
  distance: 130 - 139:  13.296
  distance: 132 - 133:   9.131
  distance: 133 - 134:  12.035
  distance: 134 - 135:   6.643
  distance: 135 - 136:  34.853
  distance: 136 - 137:  22.086
  distance: 136 - 138:  18.391
  distance: 140 - 141:  24.720
  distance: 140 - 143:  26.409
  distance: 141 - 142:   4.285
  distance: 144 - 145:   6.071
  distance: 145 - 146:  28.786
  distance: 145 - 148:  39.902
  distance: 146 - 147:  27.168
  distance: 146 - 152:  50.901
  distance: 148 - 150:  43.545
  distance: 149 - 151:  39.871
  distance: 153 - 156:  28.307
  distance: 156 - 157:  33.453
  distance: 157 - 158:  24.345
  distance: 157 - 159:  15.449
  distance: 160 - 161:  22.007
  distance: 161 - 162:   4.961
  distance: 161 - 164:  24.516
  distance: 162 - 163:  24.543
  distance: 162 - 166:  28.961
  distance: 164 - 165:  28.061
  distance: 166 - 167:  18.329
  distance: 167 - 168:  37.125
  distance: 167 - 170:  29.879
  distance: 168 - 169:  14.230
  distance: 168 - 174:  29.302
  distance: 170 - 171:  28.338