Starting phenix.real_space_refine
on Sat Aug  8 06:03:25 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8fix_29212/08_2026/8fix_29212.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fix_29212/08_2026/8fix_29212.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fix_29212/08_2026/8fix_29212.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fix_29212/08_2026/8fix_29212.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/8fix_29212/08_2026/8fix_29212.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8fix_29212/08_2026/8fix_29212.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fix_29212/08_2026/8fix_29212.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fix_29212/08_2026/8fix_29212.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.018
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P      49      5.49       5
     Mg      1      5.21       5
     S     106      5.16       5
     C   16099      2.51       5
     N    4589      2.21       5
     O    5097      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 25943
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "N"
      Number of atoms: 304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 304
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "T"
      Number of atoms: 478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 478
          Classifications: {'DNA': 23}
          Link IDs: {'rna3p': 22}
    Chain: "A"
      Number of atoms: 1768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1768
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 9, 'TRANS': 218}
    Chain: "B"
      Number of atoms: 1772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1772
          Classifications: {'peptide': 229}
          Link IDs: {'PTRANS': 9, 'TRANS': 219}
    Chain: "C"
      Number of atoms: 10407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1319, 10407
          Classifications: {'peptide': 1319}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 55, 'TRANS': 1263}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 10397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1336, 10397
          Classifications: {'peptide': 1336}
          Link IDs: {'PTRANS': 54, 'TRANS': 1281}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 232
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 232
          Classifications: {'RNAv2': 11}
          Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 6}
          Link IDs: {'rna3p': 10}
    Chain: "E"
      Number of atoms: 582
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 582
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 2, 'TRANS': 70}
    Chain: "D"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' MG': 1, ' ZN': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  15192  SG  CYS D  72     102.008 116.349  90.749  1.00152.51           S
  ATOM  15300  SG  CYS D  85     105.244 114.694  91.817  1.00144.54           S
  ATOM  15324  SG  CYS D  88     102.262 113.409  92.321  1.00142.40           S
  ATOM  21012  SG  CYS D 814      98.399  46.905  89.581  1.00 89.14           S
  ATOM  21577  SG  CYS D 888      96.216  50.059  89.744  1.00 79.14           S
  ATOM  21628  SG  CYS D 895      97.576  48.839  86.450  1.00 64.64           S
  ATOM  21649  SG  CYS D 898      94.844  46.847  88.193  1.00 65.60           S

  Time building chain proxies: 5.06, per 1000 atoms: 0.20
  Number of scatterers: 25943
  At special positions: 0
  Unit cell: (136.018, 147.594, 167.852, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S     106     16.00
     P      49     15.00
     Mg      1     11.99
     O    5097      8.00
     N    4589      7.00
     C   16099      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.10
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN D1501 "
        pdb="ZN    ZN D1501 " - pdb=" SG  CYS D  85 "
        pdb="ZN    ZN D1501 " - pdb=" SG  CYS D  88 "
        pdb="ZN    ZN D1501 " - pdb=" SG  CYS D  72 "
      pdb="  ZN D1502 "
        pdb="ZN    ZN D1502 " - pdb=" SG  CYS D 895 "
        pdb="ZN    ZN D1502 " - pdb=" SG  CYS D 814 "
        pdb="ZN    ZN D1502 " - pdb=" SG  CYS D 898 "
        pdb="ZN    ZN D1502 " - pdb=" SG  CYS D 888 "
      Number of angles added : 6


  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5880

  Finding SS restraints...
    Secondary structure from input PDB file:
      102 helices and 45 sheets defined
      38.8% alpha, 12.2% beta
      9 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 2.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 50
    Processing helix  chain 'A' and resid 77 through 87
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 154 through 162
      removed outlier: 3.826A  pdb=" N   HIS A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 233
      removed outlier: 3.590A  pdb=" N   ALA A 230 " --> pdb=" O   GLU A 226 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   PHE A 231 " --> pdb=" O   GLN A 227 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   ASP A 233 " --> pdb=" O   GLU A 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 50
    Processing helix  chain 'B' and resid 77 through 87
    Processing helix  chain 'B' and resid 111 through 115
      removed outlier: 3.540A  pdb=" N   ASP B 114 " --> pdb=" O   THR B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 154 through 161
      removed outlier: 3.610A  pdb=" N   ARG B 158 " --> pdb=" O   PRO B 154 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 230
    Processing helix  chain 'C' and resid 5 through 10
      removed outlier: 3.583A  pdb=" N   LYS C   9 " --> pdb=" O   THR C   6 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 39
    Processing helix  chain 'C' and resid 48 through 57
    Processing helix  chain 'C' and resid 81 through 89
    Processing helix  chain 'C' and resid 206 through 213
    Processing helix  chain 'C' and resid 216 through 225
    Processing helix  chain 'C' and resid 242 through 247
    Processing helix  chain 'C' and resid 270 through 281
    Processing helix  chain 'C' and resid 288 through 295
    Processing helix  chain 'C' and resid 318 through 328
    Processing helix  chain 'C' and resid 345 through 354
    Processing helix  chain 'C' and resid 358 through 371
    Processing helix  chain 'C' and resid 377 through 390
      removed outlier: 4.135A  pdb=" N   PHE C 389 " --> pdb=" O   PHE C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 398 through 409
    Processing helix  chain 'C' and resid 421 through 438
    Processing helix  chain 'C' and resid 455 through 481
      removed outlier: 4.404A  pdb=" N   ARG C 473 " --> pdb=" O   VAL C 469 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   ALA C 474 " --> pdb=" O   ARG C 470 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 488 through 493
    Processing helix  chain 'C' and resid 495 through 508
    Processing helix  chain 'C' and resid 519 through 527
    Processing helix  chain 'C' and resid 607 through 612
      removed outlier: 3.883A  pdb=" N   GLY C 612 " --> pdb=" O   ALA C 608 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 664 through 668
      removed outlier: 3.792A  pdb=" N   LEU C 667 " --> pdb=" O   GLY C 664 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE C 668 " --> pdb=" O   ALA C 665 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 664 through 668'
    Processing helix  chain 'C' and resid 670 through 674
    Processing helix  chain 'C' and resid 675 through 688
    Processing helix  chain 'C' and resid 704 through 712
    Processing helix  chain 'C' and resid 819 through 826
      removed outlier: 4.189A  pdb=" N   VAL C 823 " --> pdb=" O   SER C 819 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 858 through 863
    Processing helix  chain 'C' and resid 942 through 981
    Processing helix  chain 'C' and resid 986 through 991
    Processing helix  chain 'C' and resid 1005 through 1038
    Processing helix  chain 'C' and resid 1101 through 1106
      removed outlier: 4.199A  pdb=" N   SER C1105 " --> pdb=" O   LEU C1101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1109 through 1134
      removed outlier: 4.067A  pdb=" N   LEU C1113 " --> pdb=" O   ILE C1109 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1137 through 1151
      removed outlier: 3.751A  pdb=" N   LEU C1141 " --> pdb=" O   GLU C1137 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1160 through 1164
    Processing helix  chain 'C' and resid 1165 through 1177
    Processing helix  chain 'C' and resid 1185 through 1189
      removed outlier: 4.354A  pdb=" N   GLY C1189 " --> pdb=" O   VAL C1186 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1191 through 1202
    Processing helix  chain 'C' and resid 1238 through 1243
    Processing helix  chain 'C' and resid 1271 through 1281
    Processing helix  chain 'C' and resid 1284 through 1293
    Processing helix  chain 'C' and resid 1297 through 1311
    Processing helix  chain 'C' and resid 1320 through 1333
    Processing helix  chain 'D' and resid 26 through 34
    Processing helix  chain 'D' and resid 58 through 63
      removed outlier: 3.756A  pdb=" N   PHE D  62 " --> pdb=" O   CYS D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 96 through 101
    Processing helix  chain 'D' and resid 113 through 118
    Processing helix  chain 'D' and resid 122 through 129
    Processing helix  chain 'D' and resid 131 through 140
    Processing helix  chain 'D' and resid 161 through 172
    Processing helix  chain 'D' and resid 181 through 192
    Processing helix  chain 'D' and resid 194 through 208
    Processing helix  chain 'D' and resid 210 through 230
    Processing helix  chain 'D' and resid 233 through 238
    Processing helix  chain 'D' and resid 263 through 283
    Processing helix  chain 'D' and resid 288 through 308
    Processing helix  chain 'D' and resid 326 through 332
    Processing helix  chain 'D' and resid 336 through 341
    Processing helix  chain 'D' and resid 370 through 377
    Processing helix  chain 'D' and resid 377 through 389
    Processing helix  chain 'D' and resid 393 through 404
    Processing helix  chain 'D' and resid 406 through 418
      removed outlier: 4.031A  pdb=" N   ASP D 410 " --> pdb=" O   ALA D 406 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLU D 418 " --> pdb=" O   GLU D 414 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 450 through 458
      removed outlier: 3.702A  pdb=" N   CYS D 454 " --> pdb=" O   HIS D 450 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   ALA D 455 " --> pdb=" O   PRO D 451 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ALA D 456 " --> pdb=" O   LEU D 452 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 483
    Processing helix  chain 'D' and resid 503 through 514
    Processing helix  chain 'D' and resid 529 through 540
    Processing helix  chain 'D' and resid 573 through 582
      removed outlier: 3.672A  pdb=" N   ALA D 577 " --> pdb=" O   THR D 573 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ILE D 582 " --> pdb=" O   ILE D 578 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 597 through 613
    Processing helix  chain 'D' and resid 614 through 636
    Processing helix  chain 'D' and resid 649 through 671
      removed outlier: 3.604A  pdb=" N   GLY D 671 " --> pdb=" O   GLN D 667 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 674 through 703
    Processing helix  chain 'D' and resid 720 through 728
    Processing helix  chain 'D' and resid 733 through 742
    Processing helix  chain 'D' and resid 768 through 804
      removed outlier: 4.258A  pdb=" N   GLY D 782 " --> pdb=" O   GLY D 778 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   ALA D 787 " --> pdb=" O   LEU D 783 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   LEU D 788 " --> pdb=" O   ALA D 784 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 834 through 839
    Processing helix  chain 'D' and resid 865 through 876
    Processing helix  chain 'D' and resid 895 through 899
      removed outlier: 3.576A  pdb=" N   CYS D 898 " --> pdb=" O   CYS D 895 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 915 through 925
    Processing helix  chain 'D' and resid 926 through 928
      No H-bonds generated for 'chain 'D' and resid 926 through 928'
    Processing helix  chain 'D' and resid 1068 through 1072
      removed outlier: 3.595A  pdb=" N   GLY D1071 " --> pdb=" O   THR D1068 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   LYS D1072 " --> pdb=" O   ALA D1069 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 1068 through 1072'
    Processing helix  chain 'D' and resid 1137 through 1147
    Processing helix  chain 'D' and resid 1216 through 1225
      removed outlier: 3.639A  pdb=" N   GLY D1225 " --> pdb=" O   LEU D1221 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1225 through 1245
    Processing helix  chain 'D' and resid 1250 through 1261
    Processing helix  chain 'D' and resid 1282 through 1296
    Processing helix  chain 'D' and resid 1308 through 1313
    Processing helix  chain 'D' and resid 1318 through 1325
      removed outlier: 3.817A  pdb=" N   ALA D1322 " --> pdb=" O   SER D1318 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1328 through 1339
    Processing helix  chain 'D' and resid 1347 through 1354
    Processing helix  chain 'D' and resid 1360 through 1373
    Processing helix  chain 'E' and resid 6 through 13
    Processing helix  chain 'E' and resid 17 through 32
      removed outlier: 3.730A  pdb=" N   GLN E  29 " --> pdb=" O   ARG E  25 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 57
      removed outlier: 3.550A  pdb=" N   GLY E  57 " --> pdb=" O   GLU E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 60 through 74
      removed outlier: 3.615A  pdb=" N   GLU E  68 " --> pdb=" O   LEU E  64 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17
      removed outlier: 7.621A  pdb=" N   LEU A  13 " --> pdb=" O   GLU A  29 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLU A  29 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   ASP A  15 " --> pdb=" O   THR A  27 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA A  24 " --> pdb=" O   MET A 205 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   MET A 205 " --> pdb=" O   ALA A  24 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   LEU A 201 " --> pdb=" O   LEU A  28 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LYS A 200 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   GLU A 188 " --> pdb=" O   LYS A 200 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105
      removed outlier: 3.849A  pdb=" N   ILE A 144 " --> pdb=" O   LEU A 100 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   MET A 142 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A 104 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 8.157A  pdb=" N   SER A 141 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 5.214A  pdb=" N   ILE A  61 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   ARG A 143 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   VAL A  59 " --> pdb=" O   ARG A 143 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   LYS A 145 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   GLN A 147 " --> pdb=" O   ALA A  55 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA A  55 " --> pdb=" O   GLN A 147 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 111
      removed outlier: 4.424A  pdb=" N   CYS A 131 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 15
      removed outlier: 3.619A  pdb=" N   ASP B  15 " --> pdb=" O   THR B  27 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU B 188 " --> pdb=" O   LYS B 200 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLU B 206 " --> pdb=" O   ARG B 182 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ARG B 182 " --> pdb=" O   GLU B 206 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 54 through 56
      removed outlier: 3.728A  pdb=" N   VAL B 146 " --> pdb=" O   VAL B  98 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   VAL B  98 " --> pdb=" O   VAL B 146 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 104
    Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92
      removed outlier: 3.520A  pdb=" N   ARG B  91 " --> pdb=" O   GLU B 122 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU B 122 " --> pdb=" O   ARG B  91 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 110
      removed outlier: 3.691A  pdb=" N   CYS B 131 " --> pdb=" O   VAL B 110 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153
      removed outlier: 3.567A  pdb=" N   VAL B 153 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14
      removed outlier: 6.572A  pdb=" N   LYS C  13 " --> pdb=" O   ALA C1183 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 66 through 75
      removed outlier: 3.726A  pdb=" N   ARG C 101 " --> pdb=" O   GLN C  69 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL C  71 " --> pdb=" O   LYS C  99 " (cutoff:3.500A)
      removed outlier: 7.477A  pdb=" N   LYS C  99 " --> pdb=" O   VAL C  71 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   TYR C  73 " --> pdb=" O   ARG C  97 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   ARG C  97 " --> pdb=" O   TYR C  73 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   LEU C  75 " --> pdb=" O   PRO C  95 " (cutoff:3.500A)
      removed outlier: 7.226A  pdb=" N   ALA C  94 " --> pdb=" O   GLY C 125 " (cutoff:3.500A)
      removed outlier: 7.418A  pdb=" N   GLY C 125 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   LEU C  96 " --> pdb=" O   TYR C 123 " (cutoff:3.500A)
      removed outlier: 4.954A  pdb=" N   TYR C 123 " --> pdb=" O   LEU C  96 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   VAL C  98 " --> pdb=" O   GLU C 121 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   GLU C 121 " --> pdb=" O   VAL C  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 143 through 145
      removed outlier: 3.790A  pdb=" N   VAL C 144 " --> pdb=" O   GLN C 513 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   GLN C 513 " --> pdb=" O   VAL C 144 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'C' and resid 451 through 453
      removed outlier: 5.891A  pdb=" N   SER C 147 " --> pdb=" O   SER C 531 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158
    Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 189
      removed outlier: 3.581A  pdb=" N   ASP C 189 " --> pdb=" O   ASN C 193 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   ASN C 193 " --> pdb=" O   ASP C 189 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 255 through 257
      removed outlier: 6.568A  pdb=" N   ALA C 257 " --> pdb=" O   VAL C 261 " (cutoff:3.500A)
      removed outlier: 5.089A  pdb=" N   VAL C 261 " --> pdb=" O   ALA C 257 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 301 through 302
      removed outlier: 7.082A  pdb=" N   TYR C 301 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581
      removed outlier: 4.167A  pdb=" N   THR C 589 " --> pdb=" O   LEU C 606 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   LEU C 606 " --> pdb=" O   THR C 589 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   GLU C 602 " --> pdb=" O   LYS C 593 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581
      removed outlier: 3.713A  pdb=" N   MET C 653 " --> pdb=" O   ARG C 592 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASP C 654 " --> pdb=" O   ALA C 617 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE C 616 " --> pdb=" O   ARG C 637 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG C 637 " --> pdb=" O   ILE C 616 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL C 634 " --> pdb=" O   PHE C 645 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 717 through 718
      removed outlier: 3.847A  pdb=" N   ASP C 781 " --> pdb=" O   ALA C 718 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 749 through 752
      removed outlier: 7.439A  pdb=" N   VAL C 733 " --> pdb=" O   GLN C 725 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLN C 725 " --> pdb=" O   VAL C 733 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLU C 775 " --> pdb=" O   VAL C 724 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758
    Processing sheet with id=AC5, first strand: chain 'C' and resid 768 through 769
    Processing sheet with id=AC6, first strand: chain 'C' and resid 789 through 790
    Processing sheet with id=AC7, first strand: chain 'C' and resid 817 through 818
      removed outlier: 8.677A  pdb=" N   ILE C1096 " --> pdb=" O   ASN C 799 " (cutoff:3.500A)
      removed outlier: 5.791A  pdb=" N   ARG C 801 " --> pdb=" O   ILE C1096 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   LEU C1098 " --> pdb=" O   ARG C 801 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ALA C 803 " --> pdb=" O   LEU C1098 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   THR C1226 " --> pdb=" O   PHE C 804 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 832
    Processing sheet with id=AC9, first strand: chain 'C' and resid 835 through 841
      removed outlier: 7.075A  pdb=" N   LEU C 836 " --> pdb=" O   LYS C1051 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   LYS C1051 " --> pdb=" O   LEU C 836 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   CYS C 838 " --> pdb=" O   ILE C1049 " (cutoff:3.500A)
      removed outlier: 4.832A  pdb=" N   ILE C1049 " --> pdb=" O   CYS C 838 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   SER C 840 " --> pdb=" O   LEU C1047 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLN C 932 " --> pdb=" O   LYS C1051 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   TYR C1053 " --> pdb=" O   ASP C 930 " (cutoff:3.500A)
      removed outlier: 4.417A  pdb=" N   ASP C 930 " --> pdb=" O   TYR C1053 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 882 through 884
      removed outlier: 7.023A  pdb=" N   LEU C 918 " --> pdb=" O   LEU C 883 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 887 through 888
    Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246
    Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246
    Processing sheet with id=AD5, first strand: chain 'C' and resid 1336 through 1339
      removed outlier: 3.983A  pdb=" N   LYS D  21 " --> pdb=" O   GLU C1338 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'D' and resid 104 through 111
      removed outlier: 9.840A  pdb=" N   LEU D 107 " --> pdb=" O   PRO D 243 " (cutoff:3.500A)
      removed outlier: 10.808A  pdb=" N   SER D 109 " --> pdb=" O   VAL D 241 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   VAL D 241 " --> pdb=" O   SER D 109 " (cutoff:3.500A)
    Processing sheet with id=AD7, first strand: chain 'D' and resid 159 through 160
      removed outlier: 4.106A  pdb=" N   VAL D 145 " --> pdb=" O   LYS D 179 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LYS D 179 " --> pdb=" O   VAL D 145 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'D' and resid 368 through 369
      removed outlier: 5.879A  pdb=" N   LEU D 368 " --> pdb=" O   ILE D 442 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD8
    Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527
      removed outlier: 4.106A  pdb=" N   ARG D 551 " --> pdb=" O   LEU D 527 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'D' and resid 707 through 708
      removed outlier: 3.716A  pdb=" N   ILE D 707 " --> pdb=" O   GLU D 714 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822
      removed outlier: 3.882A  pdb=" N   VAL D 882 " --> pdb=" O   ILE D 820 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   MET D 822 " --> pdb=" O   VAL D 880 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   VAL D 880 " --> pdb=" O   MET D 822 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'D' and resid 849 through 850
      removed outlier: 4.372A  pdb=" N   ASP D 855 " --> pdb=" O   LYS D 850 " (cutoff:3.500A)
    Processing sheet with id=AE4, first strand: chain 'D' and resid 991 through 994
      removed outlier: 6.265A  pdb=" N   LEU D 984 " --> pdb=" O   LYS D 992 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   SER D 994 " --> pdb=" O   LEU D 982 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   LEU D 982 " --> pdb=" O   SER D 994 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   GLU D1009 " --> pdb=" O   ILE D 958 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'D' and resid 966 through 967
      removed outlier: 3.572A  pdb=" N   VAL D 966 " --> pdb=" O   VAL D 974 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   VAL D 974 " --> pdb=" O   VAL D 966 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'D' and resid 1026 through 1027
    Processing sheet with id=AE7, first strand: chain 'D' and resid 1077 through 1078
    Processing sheet with id=AE8, first strand: chain 'D' and resid 1188 through 1191
      removed outlier: 3.528A  pdb=" N   ILE D1190 " --> pdb=" O   ARG D1173 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'D' and resid 1279 through 1281
      removed outlier: 7.012A  pdb=" N   THR D1301 " --> pdb=" O   VAL D1267 " (cutoff:3.500A)

    996 hydrogen bonds defined for protein.
    2826 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      22 hydrogen bonds
      44 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      29 stacking parallelities
  Total time for adding SS restraints: 6.05

  Time building geometry restraints manager: 2.85 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 8775
        1.35 -     1.47: 5707
        1.47 -     1.60: 11716
        1.60 -     1.73: 47
        1.73 -     1.86: 184
  Bond restraints: 26429
  Sorted by residual:
  bond pdb=" N   PHE C 812 "
       pdb=" CA  PHE C 812 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.29e-02 6.01e+03 7.61e+00
  bond pdb=" C3'  DC T  21 "
       pdb=" C2'  DC T  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.536 -0.020 8.00e-03 1.56e+04 6.53e+00
  bond pdb=" N   PHE D1325 "
       pdb=" CA  PHE D1325 "
    ideal  model  delta    sigma   weight residual
    1.454  1.484 -0.029 1.17e-02 7.31e+03 6.30e+00
  bond pdb=" N   GLN D1326 "
       pdb=" CA  GLN D1326 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.031 1.29e-02 6.01e+03 5.94e+00
  bond pdb=" N   MET C 741 "
       pdb=" CA  MET C 741 "
    ideal  model  delta    sigma   weight residual
    1.460  1.489 -0.029 1.17e-02 7.31e+03 5.94e+00
  ... (remaining 26424 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 35457
        2.68 -     5.36: 393
        5.36 -     8.04: 48
        8.04 -    10.72: 7
       10.72 -    13.40: 1
  Bond angle restraints: 35906
  Sorted by residual:
  angle pdb=" N   ASN D 458 "
        pdb=" CA  ASN D 458 "
        pdb=" C   ASN D 458 "
      ideal   model   delta    sigma   weight residual
     111.39  103.84    7.55 1.38e+00 5.25e-01 2.99e+01
  angle pdb=" CB  MET C 239 "
        pdb=" CG  MET C 239 "
        pdb=" SD  MET C 239 "
      ideal   model   delta    sigma   weight residual
     112.70  126.10  -13.40 3.00e+00 1.11e-01 2.00e+01
  angle pdb=" CA  ARG E  67 "
        pdb=" CB  ARG E  67 "
        pdb=" CG  ARG E  67 "
      ideal   model   delta    sigma   weight residual
     114.10  122.69   -8.59 2.00e+00 2.50e-01 1.85e+01
  angle pdb=" C   GLN D1326 "
        pdb=" N   GLU D1327 "
        pdb=" CA  GLU D1327 "
      ideal   model   delta    sigma   weight residual
     120.94  127.53   -6.59 1.57e+00 4.06e-01 1.76e+01
  angle pdb=" N3   DT T   5 "
        pdb=" C4   DT T   5 "
        pdb=" O4   DT T   5 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  ... (remaining 35901 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.42: 15796
       35.42 -    70.83: 314
       70.83 -   106.25: 31
      106.25 -   141.67: 1
      141.67 -   177.09: 1
  Dihedral angle restraints: 16143
    sinusoidal: 7001
      harmonic: 9142
  Sorted by residual:
  dihedral pdb=" CA  PRO C1185 "
           pdb=" C   PRO C1185 "
           pdb=" N   VAL C1186 "
           pdb=" CA  VAL C1186 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.26  -27.74     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" CA  ALA C 746 "
           pdb=" C   ALA C 746 "
           pdb=" N   GLY C 747 "
           pdb=" CA  GLY C 747 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.24   25.76     0      5.00e+00 4.00e-02 2.66e+01
  dihedral pdb=" CA  LYS D  66 "
           pdb=" C   LYS D  66 "
           pdb=" N   ASP D  67 "
           pdb=" CA  ASP D  67 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.17  -19.83     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 16140 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 3318
       0.056 -    0.112: 657
       0.112 -    0.167: 101
       0.167 -    0.223: 15
       0.223 -    0.279: 14
  Chirality restraints: 4105
  Sorted by residual:
  chirality pdb=" CA  PHE B  35 "
            pdb=" N   PHE B  35 "
            pdb=" C   PHE B  35 "
            pdb=" CB  PHE B  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  GLU C1274 "
            pdb=" N   GLU C1274 "
            pdb=" C   GLU C1274 "
            pdb=" CB  GLU C1274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CA  ARG E  67 "
            pdb=" N   ARG E  67 "
            pdb=" C   ARG E  67 "
            pdb=" CB  ARG E  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.49e+00
  ... (remaining 4102 not shown)

  Planarity restraints: 4535
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 775 "    0.058 5.00e-02 4.00e+02   8.89e-02 1.27e+01
        pdb=" N   PRO C 776 "   -0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO C 776 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO C 776 "    0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 127 "   -0.055 5.00e-02 4.00e+02   8.13e-02 1.06e+01
        pdb=" N   PRO C 128 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO C 128 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO C 128 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  94 "    0.049 5.00e-02 4.00e+02   7.56e-02 9.13e+00
        pdb=" N   PRO C  95 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.041 5.00e-02 4.00e+02
  ... (remaining 4532 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 175
        2.53 -     3.12: 18993
        3.12 -     3.71: 40404
        3.71 -     4.31: 52890
        4.31 -     4.90: 87957
  Nonbonded interactions: 200419
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 460 "
            pdb=" OD2 ASP D 464 "
     model   vdw
     1.933 3.040
  nonbonded pdb=" CE2 PHE C 812 "
            pdb=" CB  PRO D 451 "
     model   vdw
     2.042 3.740
  nonbonded pdb=" OD1 ASP D 464 "
            pdb="MG    MG D1503 "
     model   vdw
     2.103 2.170
  nonbonded pdb=" O   PHE B  35 "
            pdb=" OG1 THR B  38 "
     model   vdw
     2.111 3.040
  nonbonded pdb=" OG  SER C 759 "
            pdb=" OG1 THR C 763 "
     model   vdw
     2.127 3.040
  ... (remaining 200414 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 7 through 232)
  selection = (chain 'B' and resid 7 through 232)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.950
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     29.430
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
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      :  0.003   0.069  26436  Z= 0.173
  Angle     :  0.710  13.404  35912  Z= 0.393
  Chirality :  0.048   0.279   4105
  Planarity :  0.005   0.089   4535
  Dihedral  : 14.304 177.085  10263
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 12.78 %
    Favored  : 87.06 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.44 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.81 (0.13), residues: 3169
  helix: -0.22 (0.14), residues: 1173
  sheet: -1.94 (0.27), residues: 326
  loop : -3.22 (0.12), residues: 1670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 170 
 TYR   0.020   0.001   TYR A 152 
 PHE   0.024   0.001   PHE C 230 
 TRP   0.040   0.002   TRP D 409 
 HIS   0.016   0.001   HIS D  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.17 (26429)
  covalent geometry    : angle       0.70963 /  0.39 (35906)
  hydrogen bonds       : bond        0.16131 / 17.43 ( 1012)
  hydrogen bonds       : angle       6.21212 /  5.05 ( 2870)
  metal coordination   : bond        0.03275 /  2.25 (    7)
  metal coordination   : angle       1.07531 /  1.89 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 374
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   86 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8120 (ttmt)
REVERT: C  239 MET cc_start: 0.7824 (mmp) cc_final: 0.7239 (mmp)
REVERT: C  285 ILE cc_start: 0.8526 (pt) cc_final: 0.8030 (mm)
REVERT: C  311 CYS cc_start: 0.6307 (p) cc_final: 0.5526 (p)
REVERT: C  547 VAL cc_start: 0.9024 (m) cc_final: 0.8810 (t)
REVERT: C  805 MET cc_start: 0.6822 (ptm) cc_final: 0.6555 (ptt)
REVERT: C  850 ILE cc_start: 0.5128 (mm) cc_final: 0.4857 (mp)
REVERT: C 1216 ARG cc_start: 0.6790 (tpt90) cc_final: 0.6586 (mtt-85)
REVERT: C 1276 TRP cc_start: 0.6255 (m-10) cc_final: 0.5863 (m-10)
REVERT: C 1304 MET cc_start: 0.6594 (tmm) cc_final: 0.6362 (ttt)
REVERT: D  180 MET cc_start: 0.3431 (tpt) cc_final: 0.2952 (tpt)
REVERT: D  330 MET cc_start: 0.7849 (ppp) cc_final: 0.7467 (ptm)
REVERT: D  973 LEU cc_start: 0.8271 (mt) cc_final: 0.7545 (mp)
REVERT: D 1040 MET cc_start: 0.1275 (mmm) cc_final: 0.0642 (mmt)
REVERT: D 1275 LEU cc_start: 0.8399 (tt) cc_final: 0.8112 (mp)
REVERT: E   30 MET cc_start: 0.4118 (mmp) cc_final: 0.3828 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 375
  average time/residue: 0.1629
  time to fit residues: 97.4557
Evaluate side-chains
  255 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 197 optimal weight:    6.9990
   chunk 215 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 132 optimal weight:    0.9990
   chunk 261 optimal weight:    0.0470
   chunk 248 optimal weight:    0.0040
   chunk 207 optimal weight:   10.0000
   chunk 155 optimal weight:    0.9990
   chunk 244 optimal weight:   10.0000
   chunk 183 optimal weight:    1.9990
   chunk 298 optimal weight:    0.6980
   overall best weight:    0.5494

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  93 GLN
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 618 GLN
C 686 GLN
C1236 ASN
D 232 ASN
** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.123705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.094311 restraints weight = 74456.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.097992 restraints weight = 41523.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.099067 restraints weight = 24989.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.099600 restraints weight = 20402.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.099780 restraints weight = 19353.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6737
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  26436  Z= 0.129
  Angle     :  0.641  11.396  35912  Z= 0.324
  Chirality :  0.045   0.314   4105
  Planarity :  0.005   0.057   4535
  Dihedral  : 10.829 176.052   4029
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.87 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.02 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.06 (0.14), residues: 3169
  helix:  0.46 (0.15), residues: 1181
  sheet: -1.44 (0.28), residues: 327
  loop : -2.86 (0.13), residues: 1661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  44 
 TYR   0.019   0.001   TYR B 177 
 PHE   0.037   0.002   PHE C 812 
 TRP   0.017   0.001   TRP C 997 
 HIS   0.010   0.001   HIS D  80 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.13 (26429)
  covalent geometry    : angle       0.64087 /  0.32 (35906)
  hydrogen bonds       : bond        0.04267 /  4.43 ( 1012)
  hydrogen bonds       : angle       4.93492 /  4.30 ( 2870)
  metal coordination   : bond        0.00306 /  0.29 (    7)
  metal coordination   : angle       2.06381 /  3.86 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 285
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  285 ILE cc_start: 0.8653 (pt) cc_final: 0.8422 (mm)
REVERT: C  850 ILE cc_start: 0.5642 (mm) cc_final: 0.5086 (mm)
REVERT: C 1216 ARG cc_start: 0.7048 (tpt90) cc_final: 0.6719 (mtt-85)
REVERT: C 1304 MET cc_start: 0.6564 (tmm) cc_final: 0.6153 (ttt)
REVERT: D   29 MET cc_start: 0.8659 (ppp) cc_final: 0.8149 (ppp)
REVERT: D  180 MET cc_start: 0.3516 (tpt) cc_final: 0.3074 (tpt)
REVERT: D  196 GLN cc_start: 0.9189 (mp10) cc_final: 0.8952 (mp10)
REVERT: D  298 MET cc_start: 0.7913 (ttm) cc_final: 0.7598 (ttp)
REVERT: D  321 LYS cc_start: 0.6940 (tptt) cc_final: 0.5838 (tptp)
REVERT: D  973 LEU cc_start: 0.8695 (mt) cc_final: 0.8124 (mp)
REVERT: D 1025 MET cc_start: 0.6722 (pmm) cc_final: 0.5977 (ppp)
REVERT: D 1099 TYR cc_start: 0.5973 (OUTLIER) cc_final: 0.4480 (m-80)
  outliers start: 31
  outliers final: 15
  residues processed: 296
  average time/residue: 0.1571
  time to fit residues: 76.0333
Evaluate side-chains
  273 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 257
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain C residue  124 MET
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  551 HIS
Chi-restraints excluded: chain C residue  618 GLN
Chi-restraints excluded: chain C residue 1273 MET
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  903 LEU
Chi-restraints excluded: chain D residue 1099 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 283 optimal weight:   20.0000
   chunk 236 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 152 optimal weight:    1.9990
   chunk 241 optimal weight:    0.2980
   chunk 213 optimal weight:    0.9980
   chunk 313 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 226 optimal weight:    0.7980
   chunk 224 optimal weight:    4.9990
   chunk 215 optimal weight:    5.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  41 ASN
A  93 GLN
B  37 HIS
C  65 ASN
** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 658 GLN
C1023 HIS
C1236 ASN
C1288 GLN
** D1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.122101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.092454 restraints weight = 74643.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.095702 restraints weight = 45201.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.096835 restraints weight = 27386.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.097294 restraints weight = 23445.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.097465 restraints weight = 20851.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6797
moved from start:          0.1714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  26436  Z= 0.119
  Angle     :  0.583  12.798  35912  Z= 0.294
  Chirality :  0.043   0.336   4105
  Planarity :  0.004   0.055   4535
  Dihedral  : 10.853 173.244   4029
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.34 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 11.45 %
    Favored  : 86.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.14), residues: 3169
  helix:  0.74 (0.15), residues: 1187
  sheet: -1.28 (0.28), residues: 342
  loop : -2.67 (0.13), residues: 1640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 148 
 TYR   0.024   0.001   TYR C1213 
 PHE   0.021   0.001   PHE C 230 
 TRP   0.010   0.001   TRP D1020 
 HIS   0.012   0.001   HIS C1023 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 (26429)
  covalent geometry    : angle       0.58263 /  0.29 (35906)
  hydrogen bonds       : bond        0.03757 /  4.00 ( 1012)
  hydrogen bonds       : angle       4.62312 /  4.09 ( 2870)
  metal coordination   : bond        0.00251 /  0.24 (    7)
  metal coordination   : angle       1.58731 /  2.93 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  314 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 267
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.7328 (t0)
REVERT: A   43 LEU cc_start: 0.4352 (OUTLIER) cc_final: 0.3941 (mm)
REVERT: A  231 PHE cc_start: 0.7460 (t80) cc_final: 0.7170 (t80)
REVERT: C  124 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.5895 (ppp)
REVERT: C  285 ILE cc_start: 0.8987 (pt) cc_final: 0.8540 (mm)
REVERT: C  850 ILE cc_start: 0.5687 (mm) cc_final: 0.5347 (mp)
REVERT: C  953 LEU cc_start: 0.8995 (tt) cc_final: 0.8626 (pp)
REVERT: C 1216 ARG cc_start: 0.7209 (tpt90) cc_final: 0.6850 (mtt-85)
REVERT: C 1304 MET cc_start: 0.6912 (tmm) cc_final: 0.6190 (ttt)
REVERT: D   29 MET cc_start: 0.8661 (ppp) cc_final: 0.8231 (ppp)
REVERT: D   80 HIS cc_start: 0.6999 (t-90) cc_final: 0.6032 (p-80)
REVERT: D  118 LYS cc_start: 0.6408 (tptm) cc_final: 0.6176 (tptt)
REVERT: D  180 MET cc_start: 0.3670 (tpt) cc_final: 0.3192 (tpt)
REVERT: D  298 MET cc_start: 0.7900 (ttm) cc_final: 0.7482 (ttp)
REVERT: D  321 LYS cc_start: 0.7119 (tptt) cc_final: 0.6003 (tptp)
REVERT: D  973 LEU cc_start: 0.8720 (mt) cc_final: 0.8149 (mp)
REVERT: D 1025 MET cc_start: 0.6853 (pmm) cc_final: 0.6200 (ppp)
REVERT: D 1040 MET cc_start: 0.2258 (mmm) cc_final: 0.1978 (mmt)
REVERT: D 1099 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.4418 (m-80)
REVERT: D 1275 LEU cc_start: 0.7780 (mp) cc_final: 0.7242 (tt)
  outliers start: 47
  outliers final: 25
  residues processed: 291
  average time/residue: 0.1650
  time to fit residues: 78.6219
Evaluate side-chains
  276 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 247
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   41 ASN
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue  124 MET
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  551 HIS
Chi-restraints excluded: chain C residue  700 VAL
Chi-restraints excluded: chain C residue  788 SER
Chi-restraints excluded: chain C residue  952 GLN
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  303 VAL
Chi-restraints excluded: chain D residue  307 LEU
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  606 ASN
Chi-restraints excluded: chain D residue  801 VAL
Chi-restraints excluded: chain D residue  903 LEU
Chi-restraints excluded: chain D residue 1034 PHE
Chi-restraints excluded: chain D residue 1099 TYR
Chi-restraints excluded: chain D residue 1107 VAL
Chi-restraints excluded: chain D residue 1342 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 302 optimal weight:    0.0060
   chunk 170 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 59 optimal weight:    9.9990
   chunk 114 optimal weight:    4.9990
   chunk 176 optimal weight:    5.9990
   chunk 287 optimal weight:   30.0000
   chunk 12 optimal weight:    3.9990
   chunk 25 optimal weight:    0.4980
   chunk 19 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    2.9002

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C 406 ASN
C 618 GLN
** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1236 ASN
D 861 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.114161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.083921 restraints weight = 76082.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.086076 restraints weight = 44851.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.087641 restraints weight = 29713.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.088286 restraints weight = 22234.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.088317 restraints weight = 20183.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7030
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.084  26436  Z= 0.226
  Angle     :  0.702  12.475  35912  Z= 0.361
  Chirality :  0.046   0.277   4105
  Planarity :  0.005   0.079   4535
  Dihedral  : 10.994 170.849   4029
  Min Nonbonded Distance : 1.767

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.53 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 13.85 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.68 (0.14), residues: 3169
  helix:  0.63 (0.15), residues: 1180
  sheet: -1.28 (0.28), residues: 349
  loop : -2.51 (0.14), residues: 1640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  91 
 TYR   0.017   0.002   TYR C1231 
 PHE   0.037   0.003   PHE D1034 
 TRP   0.012   0.002   TRP D1020 
 HIS   0.021   0.002   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00512 /  0.23 (26429)
  covalent geometry    : angle       0.70170 /  0.36 (35906)
  hydrogen bonds       : bond        0.04702 /  4.96 ( 1012)
  hydrogen bonds       : angle       4.76029 /  4.36 ( 2870)
  metal coordination   : bond        0.00678 /  0.67 (    7)
  metal coordination   : angle       2.09799 /  3.94 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 249
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.4762 (OUTLIER) cc_final: 0.4297 (mm)
REVERT: B   86 LYS cc_start: 0.8927 (mtpt) cc_final: 0.8726 (mtpt)
REVERT: C  124 MET cc_start: 0.7046 (OUTLIER) cc_final: 0.6174 (ppp)
REVERT: C  504 GLU cc_start: 0.8279 (pp20) cc_final: 0.8066 (pp20)
REVERT: C  741 MET cc_start: 0.7378 (mmm) cc_final: 0.6992 (mmt)
REVERT: C  805 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7216 (ppp)
REVERT: C  811 ASN cc_start: 0.9118 (p0) cc_final: 0.8533 (p0)
REVERT: C  850 ILE cc_start: 0.5939 (mm) cc_final: 0.5393 (mm)
REVERT: C  953 LEU cc_start: 0.9018 (tt) cc_final: 0.8595 (pp)
REVERT: C 1023 HIS cc_start: 0.8327 (m170) cc_final: 0.7958 (m90)
REVERT: C 1216 ARG cc_start: 0.6889 (tpt90) cc_final: 0.6655 (mtt-85)
REVERT: C 1304 MET cc_start: 0.6645 (tmm) cc_final: 0.5767 (tmm)
REVERT: D   29 MET cc_start: 0.8784 (ppp) cc_final: 0.8392 (ppp)
REVERT: D  180 MET cc_start: 0.4068 (tpt) cc_final: 0.3589 (tpt)
REVERT: D  298 MET cc_start: 0.8073 (ttm) cc_final: 0.7550 (ttp)
REVERT: D  321 LYS cc_start: 0.7289 (tptt) cc_final: 0.6200 (tptp)
REVERT: D  604 MET cc_start: 0.7299 (tmm) cc_final: 0.7047 (tmm)
REVERT: D  973 LEU cc_start: 0.8553 (mt) cc_final: 0.7954 (mp)
REVERT: D 1099 TYR cc_start: 0.5801 (OUTLIER) cc_final: 0.3850 (m-80)
REVERT: D 1260 MET cc_start: 0.8800 (ttm) cc_final: 0.8355 (ttp)
  outliers start: 78
  outliers final: 54
  residues processed: 289
  average time/residue: 0.1699
  time to fit residues: 80.4703
Evaluate side-chains
  292 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 234
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   74 VAL
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  124 MET
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  196 VAL
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  563 THR
Chi-restraints excluded: chain C residue  655 VAL
Chi-restraints excluded: chain C residue  700 VAL
Chi-restraints excluded: chain C residue  702 THR
Chi-restraints excluded: chain C residue  770 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  805 MET
Chi-restraints excluded: chain C residue  927 THR
Chi-restraints excluded: chain C residue 1096 ILE
Chi-restraints excluded: chain C residue 1214 ASP
Chi-restraints excluded: chain C residue 1226 THR
Chi-restraints excluded: chain C residue 1275 VAL
Chi-restraints excluded: chain C residue 1292 THR
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  303 VAL
Chi-restraints excluded: chain D residue  307 LEU
Chi-restraints excluded: chain D residue  329 ASP
Chi-restraints excluded: chain D residue  343 LEU
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  552 ILE
Chi-restraints excluded: chain D residue  606 ASN
Chi-restraints excluded: chain D residue  644 MET
Chi-restraints excluded: chain D residue  760 THR
Chi-restraints excluded: chain D residue  801 VAL
Chi-restraints excluded: chain D residue  803 VAL
Chi-restraints excluded: chain D residue  820 ILE
Chi-restraints excluded: chain D residue  886 VAL
Chi-restraints excluded: chain D residue  903 LEU
Chi-restraints excluded: chain D residue 1034 PHE
Chi-restraints excluded: chain D residue 1099 TYR
Chi-restraints excluded: chain D residue 1107 VAL
Chi-restraints excluded: chain D residue 1143 ASP
Chi-restraints excluded: chain D residue 1221 LEU
Chi-restraints excluded: chain D residue 1229 VAL
Chi-restraints excluded: chain D residue 1256 ILE
Chi-restraints excluded: chain E residue   59 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 123 optimal weight:    4.9990
   chunk 283 optimal weight:    2.9990
   chunk 191 optimal weight:    0.3980
   chunk 88 optimal weight:    0.9980
   chunk 129 optimal weight:    0.9980
   chunk 213 optimal weight:    0.9990
   chunk 214 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 226 optimal weight:    0.0570
   chunk 233 optimal weight:   10.0000
   chunk 98 optimal weight:    0.5980
   overall best weight:    0.5698

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 276 GLN
** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1236 ASN
D 300 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.117247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.087260 restraints weight = 74767.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.089403 restraints weight = 44853.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.090880 restraints weight = 30413.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.091684 restraints weight = 22796.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.091966 restraints weight = 19904.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  26436  Z= 0.110
  Angle     :  0.573  11.861  35912  Z= 0.287
  Chirality :  0.043   0.414   4105
  Planarity :  0.004   0.068   4535
  Dihedral  : 10.937 169.578   4029
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.02 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.10 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.37 (0.15), residues: 3169
  helix:  0.95 (0.15), residues: 1180
  sheet: -1.06 (0.29), residues: 343
  loop : -2.40 (0.14), residues: 1646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 481 
 TYR   0.018   0.001   TYR D 512 
 PHE   0.021   0.001   PHE D1034 
 TRP   0.014   0.001   TRP D1020 
 HIS   0.007   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 (26429)
  covalent geometry    : angle       0.57217 /  0.29 (35906)
  hydrogen bonds       : bond        0.03713 /  3.96 ( 1012)
  hydrogen bonds       : angle       4.42221 /  4.04 ( 2870)
  metal coordination   : bond        0.00171 /  0.18 (    7)
  metal coordination   : angle       1.68408 /  3.08 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 252
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.4771 (OUTLIER) cc_final: 0.4235 (mm)
REVERT: A  231 PHE cc_start: 0.7344 (t80) cc_final: 0.6987 (t80)
REVERT: C  285 ILE cc_start: 0.8964 (pt) cc_final: 0.8728 (mp)
REVERT: C  688 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7370 (pm20)
REVERT: C  741 MET cc_start: 0.7274 (mmm) cc_final: 0.6909 (mmt)
REVERT: C  805 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.7066 (ppp)
REVERT: C  811 ASN cc_start: 0.8932 (p0) cc_final: 0.8555 (p0)
REVERT: C  850 ILE cc_start: 0.5885 (mm) cc_final: 0.5568 (mp)
REVERT: C 1023 HIS cc_start: 0.8337 (m170) cc_final: 0.7880 (m90)
REVERT: C 1232 MET cc_start: 0.8130 (ppp) cc_final: 0.7721 (ppp)
REVERT: C 1304 MET cc_start: 0.6788 (tmm) cc_final: 0.5882 (tmm)
REVERT: D   29 MET cc_start: 0.8665 (ppp) cc_final: 0.8347 (ppp)
REVERT: D  180 MET cc_start: 0.3876 (tpt) cc_final: 0.3217 (tpt)
REVERT: D  298 MET cc_start: 0.7849 (ttm) cc_final: 0.7625 (ttp)
REVERT: D  321 LYS cc_start: 0.7228 (tptt) cc_final: 0.6249 (tptp)
REVERT: D  385 LEU cc_start: 0.8421 (tp) cc_final: 0.8104 (tp)
REVERT: D  604 MET cc_start: 0.7200 (tmm) cc_final: 0.6953 (tmm)
REVERT: D  973 LEU cc_start: 0.8769 (mt) cc_final: 0.8172 (mp)
REVERT: D 1025 MET cc_start: 0.6547 (ptp) cc_final: 0.5792 (ppp)
REVERT: D 1099 TYR cc_start: 0.5893 (OUTLIER) cc_final: 0.3946 (m-80)
REVERT: D 1260 MET cc_start: 0.8738 (ttm) cc_final: 0.8117 (ttp)
REVERT: D 1275 LEU cc_start: 0.7748 (mp) cc_final: 0.7276 (tt)
  outliers start: 64
  outliers final: 36
  residues processed: 295
  average time/residue: 0.1627
  time to fit residues: 79.1472
Evaluate side-chains
  280 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 240
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  563 THR
Chi-restraints excluded: chain C residue  660 VAL
Chi-restraints excluded: chain C residue  677 ASN
Chi-restraints excluded: chain C residue  688 GLN
Chi-restraints excluded: chain C residue  700 VAL
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  805 MET
Chi-restraints excluded: chain C residue  927 THR
Chi-restraints excluded: chain C residue  952 GLN
Chi-restraints excluded: chain C residue 1214 ASP
Chi-restraints excluded: chain C residue 1254 VAL
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  300 GLN
Chi-restraints excluded: chain D residue  303 VAL
Chi-restraints excluded: chain D residue  307 LEU
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  583 VAL
Chi-restraints excluded: chain D residue  606 ASN
Chi-restraints excluded: chain D residue  677 GLU
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  903 LEU
Chi-restraints excluded: chain D residue 1099 TYR
Chi-restraints excluded: chain D residue 1107 VAL
Chi-restraints excluded: chain D residue 1143 ASP
Chi-restraints excluded: chain D residue 1221 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 169 optimal weight:    9.9990
   chunk 67 optimal weight:    0.9980
   chunk 229 optimal weight:    1.9990
   chunk 305 optimal weight:    6.9990
   chunk 160 optimal weight:    0.8980
   chunk 136 optimal weight:   20.0000
   chunk 29 optimal weight:    5.9990
   chunk 247 optimal weight:    4.9990
   chunk 236 optimal weight:    0.4980
   chunk 120 optimal weight:    4.9990
   chunk 303 optimal weight:    6.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  37 HIS
B  41 ASN
C 276 GLN
** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1236 ASN
** D  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 875 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.114511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.084139 restraints weight = 75477.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.087265 restraints weight = 43391.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.088056 restraints weight = 27464.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.088766 restraints weight = 22350.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.088766 restraints weight = 19654.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.2870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  26436  Z= 0.159
  Angle     :  0.618  11.762  35912  Z= 0.311
  Chirality :  0.044   0.351   4105
  Planarity :  0.004   0.086   4535
  Dihedral  : 10.968 168.061   4029
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.37 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.32 %
    Favored  : 81.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.15), residues: 3169
  helix:  0.99 (0.15), residues: 1181
  sheet: -1.11 (0.29), residues: 337
  loop : -2.33 (0.14), residues: 1651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  33 
 TYR   0.017   0.001   TYR D1099 
 PHE   0.019   0.002   PHE D1034 
 TRP   0.013   0.001   TRP D1020 
 HIS   0.007   0.001   HIS C 551 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.16 (26429)
  covalent geometry    : angle       0.61729 /  0.31 (35906)
  hydrogen bonds       : bond        0.03964 /  4.25 ( 1012)
  hydrogen bonds       : angle       4.49312 /  4.13 ( 2870)
  metal coordination   : bond        0.00373 /  0.38 (    7)
  metal coordination   : angle       1.68076 /  3.08 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 246
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.4917 (OUTLIER) cc_final: 0.4365 (mm)
REVERT: A  231 PHE cc_start: 0.7442 (t80) cc_final: 0.7048 (t80)
REVERT: B   85 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.9018 (mm)
REVERT: C  285 ILE cc_start: 0.8977 (pt) cc_final: 0.8765 (mp)
REVERT: C  688 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7537 (pm20)
REVERT: C  741 MET cc_start: 0.7370 (mmm) cc_final: 0.7088 (mmm)
REVERT: C  805 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7134 (ppp)
REVERT: C  811 ASN cc_start: 0.8998 (p0) cc_final: 0.8599 (p0)
REVERT: C  850 ILE cc_start: 0.5970 (mm) cc_final: 0.5407 (mm)
REVERT: C  953 LEU cc_start: 0.9036 (tt) cc_final: 0.8577 (pp)
REVERT: C 1232 MET cc_start: 0.8053 (ppp) cc_final: 0.7559 (ppp)
REVERT: C 1304 MET cc_start: 0.6646 (tmm) cc_final: 0.5734 (tmm)
REVERT: D   29 MET cc_start: 0.8750 (ppp) cc_final: 0.8404 (ppp)
REVERT: D  118 LYS cc_start: 0.6993 (tptm) cc_final: 0.6781 (tptt)
REVERT: D  180 MET cc_start: 0.3603 (tpt) cc_final: 0.3159 (tpt)
REVERT: D  298 MET cc_start: 0.7861 (ttm) cc_final: 0.7467 (ttp)
REVERT: D  321 LYS cc_start: 0.7302 (tptt) cc_final: 0.6313 (tptp)
REVERT: D  385 LEU cc_start: 0.8394 (tp) cc_final: 0.8074 (tp)
REVERT: D  435 GLN cc_start: 0.6841 (OUTLIER) cc_final: 0.5104 (mp10)
REVERT: D  973 LEU cc_start: 0.8609 (mt) cc_final: 0.7924 (mp)
REVERT: D 1025 MET cc_start: 0.6683 (ptp) cc_final: 0.5895 (ppp)
  outliers start: 70
  outliers final: 50
  residues processed: 284
  average time/residue: 0.1549
  time to fit residues: 73.1726
Evaluate side-chains
  293 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 238
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   81 ILE
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   51 MET
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  563 THR
Chi-restraints excluded: chain C residue  655 VAL
Chi-restraints excluded: chain C residue  660 VAL
Chi-restraints excluded: chain C residue  677 ASN
Chi-restraints excluded: chain C residue  681 MET
Chi-restraints excluded: chain C residue  688 GLN
Chi-restraints excluded: chain C residue  700 VAL
Chi-restraints excluded: chain C residue  702 THR
Chi-restraints excluded: chain C residue  764 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  796 LEU
Chi-restraints excluded: chain C residue  805 MET
Chi-restraints excluded: chain C residue  927 THR
Chi-restraints excluded: chain C residue 1226 THR
Chi-restraints excluded: chain C residue 1254 VAL
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  303 VAL
Chi-restraints excluded: chain D residue  307 LEU
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  435 GLN
Chi-restraints excluded: chain D residue  606 ASN
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  801 VAL
Chi-restraints excluded: chain D residue  803 VAL
Chi-restraints excluded: chain D residue  885 VAL
Chi-restraints excluded: chain D residue  903 LEU
Chi-restraints excluded: chain D residue 1099 TYR
Chi-restraints excluded: chain D residue 1107 VAL
Chi-restraints excluded: chain D residue 1141 VAL
Chi-restraints excluded: chain D residue 1143 ASP
Chi-restraints excluded: chain D residue 1221 LEU
Chi-restraints excluded: chain D residue 1226 VAL
Chi-restraints excluded: chain D residue 1229 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 83 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 205 optimal weight:    0.6980
   chunk 313 optimal weight:    9.9990
   chunk 308 optimal weight:    2.9990
   chunk 291 optimal weight:    6.9990
   chunk 294 optimal weight:    6.9990
   chunk 55 optimal weight:    8.9990
   chunk 118 optimal weight:    0.8980
   chunk 238 optimal weight:    0.9980
   chunk 255 optimal weight:    2.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 276 GLN
** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1236 ASN
** D  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.114940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.084531 restraints weight = 75584.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.087137 restraints weight = 43281.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.088489 restraints weight = 27717.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.089098 restraints weight = 21770.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.089202 restraints weight = 20489.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7000
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  26436  Z= 0.131
  Angle     :  0.595  12.502  35912  Z= 0.297
  Chirality :  0.043   0.406   4105
  Planarity :  0.004   0.067   4535
  Dihedral  : 10.941 167.415   4029
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.55 %
    Favored  : 94.41 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.94 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.15), residues: 3169
  helix:  1.05 (0.15), residues: 1181
  sheet: -1.08 (0.29), residues: 335
  loop : -2.27 (0.14), residues: 1653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C1216 
 TYR   0.014   0.001   TYR D 512 
 PHE   0.018   0.001   PHE D1034 
 TRP   0.014   0.001   TRP D1020 
 HIS   0.015   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 (26429)
  covalent geometry    : angle       0.59423 /  0.30 (35906)
  hydrogen bonds       : bond        0.03788 /  4.06 ( 1012)
  hydrogen bonds       : angle       4.42805 /  4.10 ( 2870)
  metal coordination   : bond        0.00321 /  0.32 (    7)
  metal coordination   : angle       1.57225 /  2.81 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  319 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 250
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.4707 (OUTLIER) cc_final: 0.4191 (mm)
REVERT: A  135 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8039 (t0)
REVERT: A  231 PHE cc_start: 0.7437 (t80) cc_final: 0.7036 (t80)
REVERT: B   85 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8971 (mm)
REVERT: C  239 MET cc_start: 0.7690 (OUTLIER) cc_final: 0.6908 (mmp)
REVERT: C  688 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7470 (pm20)
REVERT: C  741 MET cc_start: 0.7382 (mmm) cc_final: 0.7095 (mmm)
REVERT: C  805 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6981 (ppp)
REVERT: C  811 ASN cc_start: 0.8965 (p0) cc_final: 0.8584 (p0)
REVERT: C  850 ILE cc_start: 0.5975 (mm) cc_final: 0.5422 (mm)
REVERT: C  953 LEU cc_start: 0.9016 (tt) cc_final: 0.8567 (pp)
REVERT: C 1216 ARG cc_start: 0.7089 (tpt170) cc_final: 0.6673 (tpt90)
REVERT: C 1232 MET cc_start: 0.8102 (ppp) cc_final: 0.7606 (ppp)
REVERT: C 1304 MET cc_start: 0.6712 (tmm) cc_final: 0.5804 (tmm)
REVERT: D   29 MET cc_start: 0.8718 (ppp) cc_final: 0.8364 (ppp)
REVERT: D  298 MET cc_start: 0.7829 (ttm) cc_final: 0.7583 (ttp)
REVERT: D  321 LYS cc_start: 0.7290 (tptt) cc_final: 0.6322 (tptp)
REVERT: D  385 LEU cc_start: 0.8352 (tp) cc_final: 0.8033 (tp)
REVERT: D  435 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.4760 (mp10)
REVERT: D  604 MET cc_start: 0.7215 (tmm) cc_final: 0.6949 (tmm)
REVERT: D  973 LEU cc_start: 0.8602 (mt) cc_final: 0.7892 (mp)
REVERT: D 1025 MET cc_start: 0.6731 (ptp) cc_final: 0.5936 (ppp)
REVERT: D 1275 LEU cc_start: 0.7777 (mp) cc_final: 0.7342 (tt)
  outliers start: 69
  outliers final: 48
  residues processed: 289
  average time/residue: 0.1618
  time to fit residues: 77.5328
Evaluate side-chains
  295 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 240
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain B residue   51 MET
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  229 ILE
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  515 MET
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  563 THR
Chi-restraints excluded: chain C residue  655 VAL
Chi-restraints excluded: chain C residue  677 ASN
Chi-restraints excluded: chain C residue  688 GLN
Chi-restraints excluded: chain C residue  700 VAL
Chi-restraints excluded: chain C residue  764 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  796 LEU
Chi-restraints excluded: chain C residue  805 MET
Chi-restraints excluded: chain C residue  927 THR
Chi-restraints excluded: chain C residue  952 GLN
Chi-restraints excluded: chain C residue 1254 VAL
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  201 LEU
Chi-restraints excluded: chain D residue  303 VAL
Chi-restraints excluded: chain D residue  307 LEU
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  435 GLN
Chi-restraints excluded: chain D residue  606 ASN
Chi-restraints excluded: chain D residue  677 GLU
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  801 VAL
Chi-restraints excluded: chain D residue  810 THR
Chi-restraints excluded: chain D residue  885 VAL
Chi-restraints excluded: chain D residue  903 LEU
Chi-restraints excluded: chain D residue 1099 TYR
Chi-restraints excluded: chain D residue 1107 VAL
Chi-restraints excluded: chain D residue 1143 ASP
Chi-restraints excluded: chain D residue 1221 LEU
Chi-restraints excluded: chain D residue 1226 VAL
Chi-restraints excluded: chain D residue 1229 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 218 optimal weight:    3.9990
   chunk 125 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 199 optimal weight:    8.9990
   chunk 226 optimal weight:    2.9990
   chunk 274 optimal weight:   10.0000
   chunk 308 optimal weight:    6.9990
   chunk 159 optimal weight:    0.8980
   chunk 241 optimal weight:    0.6980
   chunk 144 optimal weight:    8.9990
   chunk 264 optimal weight:    0.7980
   overall best weight:    1.2782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1023 HIS
C1236 ASN
** D  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 300 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.114614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.084240 restraints weight = 75213.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.087260 restraints weight = 43069.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.088064 restraints weight = 27715.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.088929 restraints weight = 21788.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.089000 restraints weight = 19478.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7011
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  26436  Z= 0.128
  Angle     :  0.603  12.822  35912  Z= 0.300
  Chirality :  0.044   0.396   4105
  Planarity :  0.004   0.063   4535
  Dihedral  : 10.903 166.170   4029
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.84 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.24 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.15), residues: 3169
  helix:  1.11 (0.15), residues: 1181
  sheet: -1.04 (0.29), residues: 335
  loop : -2.19 (0.14), residues: 1653

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 182 
 TYR   0.014   0.001   TYR D 512 
 PHE   0.017   0.001   PHE C 253 
 TRP   0.014   0.001   TRP D 115 
 HIS   0.012   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 (26429)
  covalent geometry    : angle       0.60240 /  0.30 (35906)
  hydrogen bonds       : bond        0.03654 /  3.93 ( 1012)
  hydrogen bonds       : angle       4.38313 /  4.10 ( 2870)
  metal coordination   : bond        0.00312 /  0.30 (    7)
  metal coordination   : angle       1.50638 /  2.66 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 253
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.4795 (OUTLIER) cc_final: 0.4233 (mm)
REVERT: A  135 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7988 (t0)
REVERT: A  231 PHE cc_start: 0.7491 (t80) cc_final: 0.7060 (t80)
REVERT: C  239 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.6906 (mmp)
REVERT: C  688 GLN cc_start: 0.7721 (OUTLIER) cc_final: 0.7398 (pm20)
REVERT: C  741 MET cc_start: 0.7081 (mmm) cc_final: 0.6875 (mmm)
REVERT: C  768 MET cc_start: 0.7711 (mtt) cc_final: 0.7507 (mtt)
REVERT: C  796 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5666 (mp)
REVERT: C  805 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7047 (ppp)
REVERT: C  811 ASN cc_start: 0.8944 (p0) cc_final: 0.8600 (p0)
REVERT: C  850 ILE cc_start: 0.5985 (mm) cc_final: 0.5664 (mp)
REVERT: C  953 LEU cc_start: 0.9015 (tt) cc_final: 0.8547 (pp)
REVERT: C 1023 HIS cc_start: 0.8367 (m90) cc_final: 0.8143 (m-70)
REVERT: C 1214 ASP cc_start: 0.8244 (t70) cc_final: 0.7811 (t70)
REVERT: C 1232 MET cc_start: 0.8141 (ppp) cc_final: 0.7660 (ppp)
REVERT: C 1304 MET cc_start: 0.6728 (tmm) cc_final: 0.5851 (tmm)
REVERT: D   29 MET cc_start: 0.8713 (ppp) cc_final: 0.8373 (ppp)
REVERT: D  115 TRP cc_start: 0.6348 (m-10) cc_final: 0.6116 (m-10)
REVERT: D  118 LYS cc_start: 0.6882 (tptt) cc_final: 0.6656 (tptm)
REVERT: D  132 LEU cc_start: 0.9142 (pt) cc_final: 0.8791 (tp)
REVERT: D  298 MET cc_start: 0.7854 (ttm) cc_final: 0.7598 (ttp)
REVERT: D  321 LYS cc_start: 0.7451 (tptt) cc_final: 0.6263 (tptp)
REVERT: D  385 LEU cc_start: 0.8366 (tp) cc_final: 0.8050 (tp)
REVERT: D  435 GLN cc_start: 0.6703 (OUTLIER) cc_final: 0.4754 (mp10)
REVERT: D  973 LEU cc_start: 0.8616 (mt) cc_final: 0.7954 (mp)
REVERT: D 1025 MET cc_start: 0.6733 (ptp) cc_final: 0.5939 (ppp)
REVERT: D 1260 MET cc_start: 0.8723 (ttm) cc_final: 0.8298 (ttp)
REVERT: D 1275 LEU cc_start: 0.7759 (mp) cc_final: 0.7320 (tt)
  outliers start: 70
  outliers final: 52
  residues processed: 292
  average time/residue: 0.1475
  time to fit residues: 70.4476
Evaluate side-chains
  299 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 240
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain B residue   26 VAL
Chi-restraints excluded: chain B residue   51 MET
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain B residue  178 SER
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue  135 THR
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  400 VAL
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  563 THR
Chi-restraints excluded: chain C residue  677 ASN
Chi-restraints excluded: chain C residue  688 GLN
Chi-restraints excluded: chain C residue  700 VAL
Chi-restraints excluded: chain C residue  764 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  796 LEU
Chi-restraints excluded: chain C residue  805 MET
Chi-restraints excluded: chain C residue  927 THR
Chi-restraints excluded: chain C residue 1254 VAL
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  249 LEU
Chi-restraints excluded: chain D residue  303 VAL
Chi-restraints excluded: chain D residue  307 LEU
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  435 GLN
Chi-restraints excluded: chain D residue  606 ASN
Chi-restraints excluded: chain D residue  677 GLU
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  760 THR
Chi-restraints excluded: chain D residue  801 VAL
Chi-restraints excluded: chain D residue  810 THR
Chi-restraints excluded: chain D residue  885 VAL
Chi-restraints excluded: chain D residue  903 LEU
Chi-restraints excluded: chain D residue 1020 TRP
Chi-restraints excluded: chain D residue 1099 TYR
Chi-restraints excluded: chain D residue 1107 VAL
Chi-restraints excluded: chain D residue 1143 ASP
Chi-restraints excluded: chain D residue 1221 LEU
Chi-restraints excluded: chain D residue 1226 VAL
Chi-restraints excluded: chain D residue 1229 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 241 optimal weight:    1.9990
   chunk 313 optimal weight:    9.9990
   chunk 49 optimal weight:    0.2980
   chunk 188 optimal weight:    2.9990
   chunk 195 optimal weight:    5.9990
   chunk 167 optimal weight:    5.9990
   chunk 12 optimal weight:    4.9990
   chunk 311 optimal weight:    8.9990
   chunk 81 optimal weight:    8.9990
   chunk 266 optimal weight:    4.9990
   overall best weight:    2.4588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  75 GLN
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN
C1236 ASN
** D  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.111737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.081211 restraints weight = 76436.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.083642 restraints weight = 44518.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.084803 restraints weight = 28705.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.085542 restraints weight = 22551.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.085595 restraints weight = 21219.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7097
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  26436  Z= 0.189
  Angle     :  0.671  12.307  35912  Z= 0.338
  Chirality :  0.045   0.357   4105
  Planarity :  0.005   0.054   4535
  Dihedral  : 10.962 165.171   4029
  Min Nonbonded Distance : 1.829

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  7.07 %
    Favored  : 92.90 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 17.46 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.30 (0.15), residues: 3169
  helix:  0.86 (0.15), residues: 1185
  sheet: -1.04 (0.28), residues: 338
  loop : -2.23 (0.14), residues: 1646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 481 
 TYR   0.019   0.002   TYR C 578 
 PHE   0.037   0.002   PHE C 230 
 TRP   0.014   0.002   TRP D1020 
 HIS   0.008   0.001   HIS C1116 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00435 /  0.19 (26429)
  covalent geometry    : angle       0.67057 /  0.34 (35906)
  hydrogen bonds       : bond        0.04231 /  4.57 ( 1012)
  hydrogen bonds       : angle       4.59199 /  4.35 ( 2870)
  metal coordination   : bond        0.00462 /  0.45 (    7)
  metal coordination   : angle       1.99573 /  3.72 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 235
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.4886 (OUTLIER) cc_final: 0.4337 (mm)
REVERT: A  135 ASP cc_start: 0.8266 (OUTLIER) cc_final: 0.8016 (t0)
REVERT: C  369 MET cc_start: 0.5279 (ptm) cc_final: 0.4829 (ptm)
REVERT: C  370 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7504 (ppp)
REVERT: C  688 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7593 (pm20)
REVERT: C  741 MET cc_start: 0.7171 (mmm) cc_final: 0.6898 (mmm)
REVERT: C  796 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5764 (mp)
REVERT: C  800 MET cc_start: 0.8014 (mmp) cc_final: 0.7792 (mmp)
REVERT: C  805 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7189 (ppp)
REVERT: C  811 ASN cc_start: 0.9012 (p0) cc_final: 0.8718 (p0)
REVERT: C  850 ILE cc_start: 0.6196 (mm) cc_final: 0.5592 (mm)
REVERT: C 1023 HIS cc_start: 0.8408 (m90) cc_final: 0.8178 (m-70)
REVERT: C 1214 ASP cc_start: 0.8316 (t70) cc_final: 0.7827 (t70)
REVERT: C 1216 ARG cc_start: 0.7618 (tpt170) cc_final: 0.7108 (mtt90)
REVERT: C 1230 MET cc_start: 0.6769 (tmm) cc_final: 0.6543 (tmm)
REVERT: C 1232 MET cc_start: 0.8072 (ppp) cc_final: 0.7536 (ppp)
REVERT: C 1304 MET cc_start: 0.6792 (tmm) cc_final: 0.5916 (tmm)
REVERT: C 1315 MET cc_start: 0.6647 (tmm) cc_final: 0.6142 (ttp)
REVERT: D   29 MET cc_start: 0.8754 (ppp) cc_final: 0.8400 (ppp)
REVERT: D  115 TRP cc_start: 0.6469 (m-10) cc_final: 0.6220 (m-10)
REVERT: D  235 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.8190 (pm20)
REVERT: D  298 MET cc_start: 0.7850 (ttm) cc_final: 0.7561 (ttp)
REVERT: D  321 LYS cc_start: 0.7336 (tptt) cc_final: 0.6390 (tptp)
REVERT: D  385 LEU cc_start: 0.8402 (tp) cc_final: 0.8067 (tp)
REVERT: D  435 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.5112 (mp10)
REVERT: D  973 LEU cc_start: 0.8535 (mt) cc_final: 0.7867 (mp)
REVERT: D 1025 MET cc_start: 0.6743 (ptp) cc_final: 0.5910 (ppp)
REVERT: D 1040 MET cc_start: 0.0915 (mmt) cc_final: 0.0403 (mmm)
REVERT: D 1143 ASP cc_start: 0.6228 (OUTLIER) cc_final: 0.5687 (t70)
  outliers start: 72
  outliers final: 53
  residues processed: 278
  average time/residue: 0.1655
  time to fit residues: 76.4103
Evaluate side-chains
  288 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 226
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain B residue   51 MET
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  101 THR
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue   87 ILE
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  370 MET
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  400 VAL
Chi-restraints excluded: chain C residue  429 MET
Chi-restraints excluded: chain C residue  515 MET
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  563 THR
Chi-restraints excluded: chain C residue  677 ASN
Chi-restraints excluded: chain C residue  681 MET
Chi-restraints excluded: chain C residue  688 GLN
Chi-restraints excluded: chain C residue  764 CYS
Chi-restraints excluded: chain C residue  770 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  796 LEU
Chi-restraints excluded: chain C residue  805 MET
Chi-restraints excluded: chain C residue  884 VAL
Chi-restraints excluded: chain C residue  927 THR
Chi-restraints excluded: chain C residue 1225 VAL
Chi-restraints excluded: chain C residue 1254 VAL
Chi-restraints excluded: chain C residue 1275 VAL
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  145 VAL
Chi-restraints excluded: chain D residue  235 GLU
Chi-restraints excluded: chain D residue  300 GLN
Chi-restraints excluded: chain D residue  303 VAL
Chi-restraints excluded: chain D residue  307 LEU
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  435 GLN
Chi-restraints excluded: chain D residue  606 ASN
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  760 THR
Chi-restraints excluded: chain D residue  801 VAL
Chi-restraints excluded: chain D residue  885 VAL
Chi-restraints excluded: chain D residue  903 LEU
Chi-restraints excluded: chain D residue 1020 TRP
Chi-restraints excluded: chain D residue 1099 TYR
Chi-restraints excluded: chain D residue 1107 VAL
Chi-restraints excluded: chain D residue 1143 ASP
Chi-restraints excluded: chain D residue 1221 LEU
Chi-restraints excluded: chain D residue 1226 VAL
Chi-restraints excluded: chain D residue 1229 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 177 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 171 optimal weight:    5.9990
   chunk 280 optimal weight:   30.0000
   chunk 200 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 HIS
C1236 ASN
** D  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.112898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.082406 restraints weight = 75303.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.085266 restraints weight = 43471.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.086075 restraints weight = 27666.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.086760 restraints weight = 22590.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.086921 restraints weight = 20218.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  26436  Z= 0.140
  Angle     :  0.631  13.194  35912  Z= 0.315
  Chirality :  0.044   0.369   4105
  Planarity :  0.004   0.057   4535
  Dihedral  : 10.919 164.664   4029
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  6.06 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.68 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.19 (0.15), residues: 3169
  helix:  0.96 (0.15), residues: 1179
  sheet: -1.03 (0.28), residues: 338
  loop : -2.16 (0.14), residues: 1652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.000   ARG B  33 
 TYR   0.015   0.001   TYR D 512 
 PHE   0.030   0.001   PHE C 230 
 TRP   0.014   0.001   TRP D1020 
 HIS   0.007   0.001   HIS D 777 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.14 (26429)
  covalent geometry    : angle       0.63023 /  0.32 (35906)
  hydrogen bonds       : bond        0.03877 /  4.20 ( 1012)
  hydrogen bonds       : angle       4.47857 /  4.26 ( 2870)
  metal coordination   : bond        0.00358 /  0.35 (    7)
  metal coordination   : angle       1.68264 /  3.06 (    6)

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

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

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6338 Ramachandran restraints generated.
    3169 Oldfield, 0 Emsley, 3169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 234
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LEU cc_start: 0.4802 (OUTLIER) cc_final: 0.4289 (mm)
REVERT: A  135 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.7978 (t0)
REVERT: A  231 PHE cc_start: 0.7434 (t80) cc_final: 0.7031 (t80)
REVERT: C  239 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6735 (mmp)
REVERT: C  369 MET cc_start: 0.5958 (ptm) cc_final: 0.5360 (ptm)
REVERT: C  370 MET cc_start: 0.8232 (mmt) cc_final: 0.7772 (ppp)
REVERT: C  741 MET cc_start: 0.7135 (mmm) cc_final: 0.6892 (mmm)
REVERT: C  768 MET cc_start: 0.7775 (mtt) cc_final: 0.7545 (mtp)
REVERT: C  796 LEU cc_start: 0.6516 (OUTLIER) cc_final: 0.5719 (mp)
REVERT: C  805 MET cc_start: 0.7428 (OUTLIER) cc_final: 0.7043 (ppp)
REVERT: C  811 ASN cc_start: 0.8953 (p0) cc_final: 0.8657 (p0)
REVERT: C  850 ILE cc_start: 0.6133 (mm) cc_final: 0.5836 (mp)
REVERT: C 1023 HIS cc_start: 0.8430 (m90) cc_final: 0.8184 (m-70)
REVERT: C 1216 ARG cc_start: 0.7518 (tpt170) cc_final: 0.7130 (mtt180)
REVERT: C 1232 MET cc_start: 0.8183 (ppp) cc_final: 0.7707 (ppp)
REVERT: C 1315 MET cc_start: 0.6592 (tmm) cc_final: 0.6054 (ttp)
REVERT: D   29 MET cc_start: 0.8717 (ppp) cc_final: 0.8402 (ppp)
REVERT: D  115 TRP cc_start: 0.6405 (m-10) cc_final: 0.6157 (m-10)
REVERT: D  132 LEU cc_start: 0.9024 (pt) cc_final: 0.8653 (tp)
REVERT: D  298 MET cc_start: 0.7909 (ttm) cc_final: 0.7575 (ttp)
REVERT: D  321 LYS cc_start: 0.7400 (tptt) cc_final: 0.6312 (tptp)
REVERT: D  385 LEU cc_start: 0.8365 (tp) cc_final: 0.8046 (tp)
REVERT: D  435 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.4888 (mp10)
REVERT: D  973 LEU cc_start: 0.8510 (mt) cc_final: 0.7851 (mp)
REVERT: D 1025 MET cc_start: 0.6739 (ptp) cc_final: 0.5905 (ppp)
REVERT: D 1040 MET cc_start: 0.1081 (mmt) cc_final: 0.0599 (mmm)
REVERT: D 1143 ASP cc_start: 0.6182 (OUTLIER) cc_final: 0.5646 (t70)
REVERT: D 1275 LEU cc_start: 0.7946 (mp) cc_final: 0.7414 (tt)
  outliers start: 64
  outliers final: 52
  residues processed: 273
  average time/residue: 0.1689
  time to fit residues: 76.4143
Evaluate side-chains
  288 residues out of total 2715 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 229
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   43 LEU
Chi-restraints excluded: chain A residue   54 CYS
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  128 HIS
Chi-restraints excluded: chain A residue  135 ASP
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain B residue   37 HIS
Chi-restraints excluded: chain B residue   51 MET
Chi-restraints excluded: chain B residue   83 LEU
Chi-restraints excluded: chain B residue   99 ILE
Chi-restraints excluded: chain B residue  129 VAL
Chi-restraints excluded: chain B residue  146 VAL
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   71 VAL
Chi-restraints excluded: chain C residue  194 LEU
Chi-restraints excluded: chain C residue  239 MET
Chi-restraints excluded: chain C residue  388 LEU
Chi-restraints excluded: chain C residue  400 VAL
Chi-restraints excluded: chain C residue  448 LEU
Chi-restraints excluded: chain C residue  515 MET
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  563 THR
Chi-restraints excluded: chain C residue  677 ASN
Chi-restraints excluded: chain C residue  688 GLN
Chi-restraints excluded: chain C residue  692 THR
Chi-restraints excluded: chain C residue  764 CYS
Chi-restraints excluded: chain C residue  782 VAL
Chi-restraints excluded: chain C residue  796 LEU
Chi-restraints excluded: chain C residue  805 MET
Chi-restraints excluded: chain C residue  884 VAL
Chi-restraints excluded: chain C residue  927 THR
Chi-restraints excluded: chain C residue 1254 VAL
Chi-restraints excluded: chain C residue 1275 VAL
Chi-restraints excluded: chain D residue   65 VAL
Chi-restraints excluded: chain D residue  109 SER
Chi-restraints excluded: chain D residue  111 THR
Chi-restraints excluded: chain D residue  145 VAL
Chi-restraints excluded: chain D residue  249 LEU
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  300 GLN
Chi-restraints excluded: chain D residue  303 VAL
Chi-restraints excluded: chain D residue  307 LEU
Chi-restraints excluded: chain D residue  422 LEU
Chi-restraints excluded: chain D residue  435 GLN
Chi-restraints excluded: chain D residue  606 ASN
Chi-restraints excluded: chain D residue  677 GLU
Chi-restraints excluded: chain D residue  743 MET
Chi-restraints excluded: chain D residue  760 THR
Chi-restraints excluded: chain D residue  801 VAL
Chi-restraints excluded: chain D residue  885 VAL
Chi-restraints excluded: chain D residue  903 LEU
Chi-restraints excluded: chain D residue 1020 TRP
Chi-restraints excluded: chain D residue 1099 TYR
Chi-restraints excluded: chain D residue 1107 VAL
Chi-restraints excluded: chain D residue 1143 ASP
Chi-restraints excluded: chain D residue 1221 LEU
Chi-restraints excluded: chain D residue 1226 VAL
Chi-restraints excluded: chain D residue 1229 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 319
   random chunks:
   chunk 169 optimal weight:    9.9990
   chunk 124 optimal weight:    0.5980
   chunk 221 optimal weight:    0.7980
   chunk 231 optimal weight:    6.9990
   chunk 294 optimal weight:   10.0000
   chunk 291 optimal weight:   10.0000
   chunk 239 optimal weight:    0.9990
   chunk 56 optimal weight:    0.4980
   chunk 129 optimal weight:    0.0020
   chunk 269 optimal weight:    0.9990
   chunk 157 optimal weight:    0.6980
   overall best weight:    0.5188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 HIS
C 276 GLN
C1236 ASN
** D  80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.114444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.084110 restraints weight = 74624.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.086512 restraints weight = 42485.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.087812 restraints weight = 27839.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.088441 restraints weight = 22016.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.088619 restraints weight = 20505.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7012
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  26436  Z= 0.114
  Angle     :  0.613  13.610  35912  Z= 0.305
  Chirality :  0.044   0.381   4105
  Planarity :  0.004   0.058   4535
  Dihedral  : 10.861 164.133   4029
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.03 %
    Allowed  :  5.52 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 18.01 %
    Favored  : 79.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.15), residues: 3169
  helix:  1.09 (0.15), residues: 1179
  sheet: -0.96 (0.29), residues: 330
  loop : -2.08 (0.14), residues: 1660

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 481 
 TYR   0.019   0.001   TYR D 512 
 PHE   0.030   0.001   PHE C 230 
 TRP   0.013   0.001   TRP D1020 
 HIS   0.018   0.001   HIS B  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00249 /  0.11 (26429)
  covalent geometry    : angle       0.61318 /  0.31 (35906)
  hydrogen bonds       : bond        0.03589 /  3.90 ( 1012)
  hydrogen bonds       : angle       4.36923 /  4.14 ( 2870)
  metal coordination   : bond        0.00241 /  0.21 (    7)
  metal coordination   : angle       1.45303 /  2.51 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4378.05 seconds
wall clock time: 76 minutes 23.42 seconds (4583.42 seconds total)