Starting phenix.real_space_refine
on Wed Jul 30 02:58:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xfb_38300/07_2025/8xfb_38300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xfb_38300/07_2025/8xfb_38300.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xfb_38300/07_2025/8xfb_38300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xfb_38300/07_2025/8xfb_38300.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xfb_38300/07_2025/8xfb_38300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xfb_38300/07_2025/8xfb_38300.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    7555      2.51       5
     N    2043      2.21       5
     O    2176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11837
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "D"
      Number of atoms: 1147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 1147
          Classifications: {'peptide': 144}
          Link IDs: {'PTRANS': 2, 'TRANS': 141}
    Chain: "A"
      Number of atoms: 2485
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 314, 2485
          Classifications: {'peptide': 314}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 297}
          Chain breaks: 7
    Chain: "B"
      Number of atoms: 8205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1038, 8205
          Classifications: {'peptide': 1038}
          Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 996}
          Chain breaks: 8
  Time building chain proxies: 7.85, per 1000 atoms: 0.66
  Number of scatterers: 11837
  At special positions: 0
  Unit cell: (102.85, 113.9, 173.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    2176      8.00
     N    2043      7.00
     C    7555      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS D1029 " - pdb=" SG  CYS B1029 " distance=2.02

  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: 2.37
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2834

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 19 sheets defined
      37.0% alpha, 19.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.95
  Creating SS restraints...
    Processing helix  chain 'D' and resid 973 through 990
      removed outlier: 3.513A  pdb=" N   LYS D 990 " --> pdb=" O   LEU D 986 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 993 through 1007
      removed outlier: 4.404A  pdb=" N   LYS D 999 " --> pdb=" O   ASP D 995 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1012 through 1018
      removed outlier: 3.723A  pdb=" N   LEU D1016 " --> pdb=" O   ARG D1012 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1026 through 1040
    Processing helix  chain 'D' and resid 1048 through 1061
      removed outlier: 3.633A  pdb=" N   GLY D1061 " --> pdb=" O   MET D1057 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1062 through 1074
      removed outlier: 3.716A  pdb=" N   GLY D1066 " --> pdb=" O   LYS D1062 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ASP D1074 " --> pdb=" O   LEU D1070 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1076 through 1087
    Processing helix  chain 'D' and resid 1088 through 1099
    Processing helix  chain 'D' and resid 1101 through 1116
      removed outlier: 3.703A  pdb=" N   ALA D1106 " --> pdb=" O   PRO D1102 " (cutoff:3.500A)
      removed outlier: 4.772A  pdb=" N   ASP D1107 " --> pdb=" O   GLU D1103 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL D1108 " --> pdb=" O   GLU D1104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 4.052A  pdb=" N   THR A 387 " --> pdb=" O   ASP A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 409
      removed outlier: 4.253A  pdb=" N   THR A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 425
      removed outlier: 4.290A  pdb=" N   SER A 419 " --> pdb=" O   GLU A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 450
      removed outlier: 3.642A  pdb=" N   LEU A 445 " --> pdb=" O   HIS A 441 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ARG A 446 " --> pdb=" O   ALA A 442 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ASN A 447 " --> pdb=" O   LEU A 443 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR A 448 " --> pdb=" O   THR A 444 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   LEU A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 543
      removed outlier: 3.813A  pdb=" N   LYS A 535 " --> pdb=" O   SER A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 565
    Processing helix  chain 'A' and resid 587 through 595
      removed outlier: 3.541A  pdb=" N   ASP A 593 " --> pdb=" O   THR A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 645
      removed outlier: 3.710A  pdb=" N   ASN A 645 " --> pdb=" O   GLN A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 720
      removed outlier: 3.757A  pdb=" N   TRP A 720 " --> pdb=" O   GLU A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 748
      removed outlier: 3.550A  pdb=" N   HIS A 747 " --> pdb=" O   LYS A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 776
      removed outlier: 4.496A  pdb=" N   ASN A 757 " --> pdb=" O   GLU A 753 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LEU A 758 " --> pdb=" O   SER A 754 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU A 759 " --> pdb=" O   LEU A 755 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   HIS A 760 " --> pdb=" O   GLN A 756 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LYS A 764 " --> pdb=" O   HIS A 760 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   SER A 766 " --> pdb=" O   SER A 762 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   LEU A 767 " --> pdb=" O   ARG A 763 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 24
      removed outlier: 3.802A  pdb=" N   LYS B  24 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 430
      removed outlier: 4.140A  pdb=" N   SER B 426 " --> pdb=" O   PRO B 423 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   LEU B 427 " --> pdb=" O   ASP B 424 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   ASP B 428 " --> pdb=" O   LEU B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 484
      removed outlier: 3.703A  pdb=" N   TYR B 484 " --> pdb=" O   ILE B 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 843 through 847
    Processing helix  chain 'B' and resid 848 through 861
      removed outlier: 3.805A  pdb=" N   LEU B 853 " --> pdb=" O   PRO B 849 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ALA B 854 " --> pdb=" O   ARG B 850 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 871 through 875
      removed outlier: 3.755A  pdb=" N   HIS B 874 " --> pdb=" O   ASP B 871 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 880 through 893
    Processing helix  chain 'B' and resid 895 through 903
    Processing helix  chain 'B' and resid 908 through 921
    Processing helix  chain 'B' and resid 923 through 941
    Processing helix  chain 'B' and resid 972 through 990
      removed outlier: 3.652A  pdb=" N   PHE B 979 " --> pdb=" O   TYR B 975 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN B 987 " --> pdb=" O   ARG B 983 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LYS B 990 " --> pdb=" O   LEU B 986 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 993 through 1008
    Processing helix  chain 'B' and resid 1009 through 1018
      removed outlier: 4.590A  pdb=" N   GLN B1015 " --> pdb=" O   ASP B1011 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   LEU B1016 " --> pdb=" O   ARG B1012 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1026 through 1040
      removed outlier: 3.698A  pdb=" N   THR B1038 " --> pdb=" O   ALA B1034 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR B1039 " --> pdb=" O   CYS B1035 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1044 through 1046
      No H-bonds generated for 'chain 'B' and resid 1044 through 1046'
    Processing helix  chain 'B' and resid 1047 through 1060
    Processing helix  chain 'B' and resid 1063 through 1074
      removed outlier: 3.948A  pdb=" N   LEU B1069 " --> pdb=" O   GLU B1065 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ASP B1074 " --> pdb=" O   LEU B1070 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1076 through 1086
    Processing helix  chain 'B' and resid 1088 through 1099
    Processing helix  chain 'B' and resid 1104 through 1117
      removed outlier: 3.655A  pdb=" N   VAL B1108 " --> pdb=" O   GLU B1104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1123 through 1135
      removed outlier: 3.512A  pdb=" N   LEU B1129 " --> pdb=" O   SER B1125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1136 through 1147
    Processing helix  chain 'B' and resid 1149 through 1164
      removed outlier: 3.783A  pdb=" N   LEU B1155 " --> pdb=" O   ASP B1151 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1172 through 1191
    Processing helix  chain 'B' and resid 1192 through 1204
      removed outlier: 3.623A  pdb=" N   ALA B1196 " --> pdb=" O   PHE B1192 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY B1204 " --> pdb=" O   ALA B1200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1207 through 1215
    Processing sheet with id=AA1, first strand: chain 'A' and resid 378 through 380
      removed outlier: 6.749A  pdb=" N   LEU A 501 " --> pdb=" O   ILE A 522 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 412
    Processing sheet with id=AA3, first strand: chain 'A' and resid 504 through 505
    Processing sheet with id=AA4, first strand: chain 'A' and resid 580 through 583
      removed outlier: 6.781A  pdb=" N   ARG A 569 " --> pdb=" O   HIS A 605 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL A 600 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 612 through 618
      removed outlier: 3.502A  pdb=" N   VAL A 614 " --> pdb=" O   MET A 658 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE A 618 " --> pdb=" O   GLY A 654 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   GLY A 654 " --> pdb=" O   PHE A 618 " (cutoff:3.500A)
      removed outlier: 7.119A  pdb=" N   TYR A 655 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
      removed outlier: 4.957A  pdb=" N   LEU A 725 " --> pdb=" O   TYR A 655 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   THR A 657 " --> pdb=" O   LEU A 723 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 14 through 15
      removed outlier: 3.862A  pdb=" N   ASP B 800 " --> pdb=" O   ALA B 812 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29
      removed outlier: 6.428A  pdb=" N   VAL B  43 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   VAL B  56 " --> pdb=" O   VAL B  43 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   VAL B  45 " --> pdb=" O   LEU B  54 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 69
      removed outlier: 3.628A  pdb=" N   LYS B  66 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   LYS B  94 " --> pdb=" O   ASP B  90 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ILE B  95 " --> pdb=" O   GLU B 108 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   GLU B 108 " --> pdb=" O   ILE B  95 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   VAL B  97 " --> pdb=" O   GLN B 106 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL B 104 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 119 through 121
      removed outlier: 4.212A  pdb=" N   TRP B 153 " --> pdb=" O   LEU B 143 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 166
      removed outlier: 6.985A  pdb=" N   LEU B 177 " --> pdb=" O   LEU B 162 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   PHE B 164 " --> pdb=" O   THR B 175 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   THR B 175 " --> pdb=" O   PHE B 164 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 249 through 252
      removed outlier: 4.221A  pdb=" N   GLN B 249 " --> pdb=" O   LEU B 263 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B 251 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   MET B 260 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLY B 280 " --> pdb=" O   ILE B 270 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   ASP B 272 " --> pdb=" O   THR B 278 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   THR B 278 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 291 through 296
      removed outlier: 7.026A  pdb=" N   ILE B 312 " --> pdb=" O   GLN B 346 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   GLN B 346 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   LEU B 314 " --> pdb=" O   ARG B 344 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 358 through 363
      removed outlier: 3.982A  pdb=" N   SER B 360 " --> pdb=" O   VAL B 374 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   VAL B 380 " --> pdb=" O   LEU B 459 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   LEU B 459 " --> pdb=" O   VAL B 380 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ILE B 382 " --> pdb=" O   THR B 457 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 470 through 472
      removed outlier: 6.604A  pdb=" N   VAL B 497 " --> pdb=" O   GLU B 510 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLU B 510 " --> pdb=" O   VAL B 497 " (cutoff:3.500A)
      removed outlier: 6.796A  pdb=" N   VAL B 499 " --> pdb=" O   HIS B 508 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 518 through 523
      removed outlier: 7.012A  pdb=" N   VAL B 518 " --> pdb=" O   THR B 534 " (cutoff:3.500A)
      removed outlier: 7.546A  pdb=" N   THR B 534 " --> pdb=" O   VAL B 518 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLY B 520 " --> pdb=" O   PHE B 532 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 571 through 576
      removed outlier: 4.937A  pdb=" N   MET B 573 " --> pdb=" O   VAL B 586 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   VAL B 586 " --> pdb=" O   MET B 573 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   LEU B 594 " --> pdb=" O   LEU B 603 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 615 through 618
      removed outlier: 3.599A  pdb=" N   ALA B 615 " --> pdb=" O   THR B 682 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 717 through 719
      removed outlier: 3.712A  pdb=" N   LEU B 732 " --> pdb=" O   ILE B 745 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ILE B 745 " --> pdb=" O   LEU B 732 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ARG B 743 " --> pdb=" O   PHE B 734 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 754 through 757
      removed outlier: 3.819A  pdb=" N   LYS B 754 " --> pdb=" O   MET B 769 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   GLY B 773 " --> pdb=" O   TYR B 770 " (cutoff:3.500A)
      removed outlier: 6.985A  pdb=" N   ALA B 774 " --> pdb=" O   SER B 787 " (cutoff:3.500A)
      removed outlier: 5.152A  pdb=" N   SER B 787 " --> pdb=" O   ALA B 774 " (cutoff:3.500A)
      removed outlier: 7.135A  pdb=" N   VAL B 776 " --> pdb=" O   VAL B 785 " (cutoff:3.500A)

    490 hydrogen bonds defined for protein.
    1380 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.16

  Time building geometry restraints manager: 2.94 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2387
        1.33 -     1.45: 2920
        1.45 -     1.58: 6688
        1.58 -     1.71: 0
        1.71 -     1.83: 86
  Bond restraints: 12081
  Sorted by residual:
  bond pdb=" N   ASP B 589 "
       pdb=" CA  ASP B 589 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.039 1.29e-02 6.01e+03 9.24e+00
  bond pdb=" N   LEU B 592 "
       pdb=" CA  LEU B 592 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.034 1.27e-02 6.20e+03 7.04e+00
  bond pdb=" C   PRO B 591 "
       pdb=" O   PRO B 591 "
    ideal  model  delta    sigma   weight residual
    1.235  1.203  0.032 1.30e-02 5.92e+03 5.97e+00
  bond pdb=" N   LEU B 594 "
       pdb=" CA  LEU B 594 "
    ideal  model  delta    sigma   weight residual
    1.456  1.484 -0.028 1.29e-02 6.01e+03 4.59e+00
  bond pdb=" N   GLU B 593 "
       pdb=" CA  GLU B 593 "
    ideal  model  delta    sigma   weight residual
    1.458  1.483 -0.025 1.19e-02 7.06e+03 4.43e+00
  ... (remaining 12076 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 16002
        1.44 -     2.89: 314
        2.89 -     4.33: 52
        4.33 -     5.78: 14
        5.78 -     7.22: 5
  Bond angle restraints: 16387
  Sorted by residual:
  angle pdb=" N   VAL B 275 "
        pdb=" CA  VAL B 275 "
        pdb=" C   VAL B 275 "
      ideal   model   delta    sigma   weight residual
     112.96  109.13    3.83 1.00e+00 1.00e+00 1.47e+01
  angle pdb=" C   GLU B 593 "
        pdb=" CA  GLU B 593 "
        pdb=" CB  GLU B 593 "
      ideal   model   delta    sigma   weight residual
     110.14  104.88    5.26 1.60e+00 3.91e-01 1.08e+01
  angle pdb=" CA  LEU B 592 "
        pdb=" C   LEU B 592 "
        pdb=" O   LEU B 592 "
      ideal   model   delta    sigma   weight residual
     121.56  118.01    3.55 1.09e+00 8.42e-01 1.06e+01
  angle pdb=" N   PRO B 591 "
        pdb=" CA  PRO B 591 "
        pdb=" C   PRO B 591 "
      ideal   model   delta    sigma   weight residual
     112.47  118.58   -6.11 2.06e+00 2.36e-01 8.79e+00
  angle pdb=" CA  LEU B 594 "
        pdb=" C   LEU B 594 "
        pdb=" O   LEU B 594 "
      ideal   model   delta    sigma   weight residual
     120.54  117.22    3.32 1.13e+00 7.83e-01 8.63e+00
  ... (remaining 16382 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 6489
       17.44 -    34.87: 615
       34.87 -    52.31: 102
       52.31 -    69.75: 18
       69.75 -    87.18: 16
  Dihedral angle restraints: 7240
    sinusoidal: 2885
      harmonic: 4355
  Sorted by residual:
  dihedral pdb=" CA  ASP B1074 "
           pdb=" C   ASP B1074 "
           pdb=" N   LYS B1075 "
           pdb=" CA  LYS B1075 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.43  -22.57     0      5.00e+00 4.00e-02 2.04e+01
  dihedral pdb=" CB  CYS D1029 "
           pdb=" SG  CYS D1029 "
           pdb=" SG  CYS B1029 "
           pdb=" CB  CYS B1029 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -119.97   33.97     1      1.00e+01 1.00e-02 1.64e+01
  dihedral pdb=" CA  CYS D1029 "
           pdb=" CB  CYS D1029 "
           pdb=" SG  CYS D1029 "
           pdb=" SG  CYS B1029 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00    7.72   71.28     1      2.00e+01 2.50e-03 1.63e+01
  ... (remaining 7237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1705
       0.062 -    0.125: 180
       0.125 -    0.187: 2
       0.187 -    0.250: 0
       0.250 -    0.312: 2
  Chirality restraints: 1889
  Sorted by residual:
  chirality pdb=" CA  GLU B 593 "
            pdb=" N   GLU B 593 "
            pdb=" C   GLU B 593 "
            pdb=" CB  GLU B 593 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.44e+00
  chirality pdb=" CB  ILE B1073 "
            pdb=" CA  ILE B1073 "
            pdb=" CG1 ILE B1073 "
            pdb=" CG2 ILE B1073 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CA  ILE A 729 "
            pdb=" N   ILE A 729 "
            pdb=" C   ILE A 729 "
            pdb=" CB  ILE A 729 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.05e-01
  ... (remaining 1886 not shown)

  Planarity restraints: 2070
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 877 "   -0.069 5.00e-02 4.00e+02   1.06e-01 1.78e+01
        pdb=" N   PRO B 878 "    0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO B 878 "   -0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO B 878 "   -0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 582 "   -0.070 5.00e-02 4.00e+02   1.05e-01 1.78e+01
        pdb=" N   PRO A 583 "    0.182 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "   -0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 465 "   -0.058 5.00e-02 4.00e+02   8.88e-02 1.26e+01
        pdb=" N   PRO B 466 "    0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO B 466 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO B 466 "   -0.048 5.00e-02 4.00e+02
  ... (remaining 2067 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 172
        2.69 -     3.24: 10664
        3.24 -     3.79: 16798
        3.79 -     4.35: 22700
        4.35 -     4.90: 37983
  Nonbonded interactions: 88317
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 426 "
            pdb=" OD1 ASP B 428 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" NH1 ARG B 604 "
            pdb=" O   GLU B 605 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" ND2 ASN B  23 "
            pdb=" O   VAL B  64 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" O   LEU D 981 "
            pdb=" ND2 ASN D 985 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" OG  SER B 786 "
            pdb=" O   MET B 823 "
     model   vdw
     2.341 3.040
  ... (remaining 88312 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     33.130
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.150
  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:             0.020
  Load rotamer database and sin/cos tables:4.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
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      :  0.002   0.057  12082  Z= 0.116
  Angle     :  0.515   7.221  16389  Z= 0.284
  Chirality :  0.039   0.312   1889
  Planarity :  0.005   0.106   2070
  Dihedral  : 14.022  87.185   4403
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.61 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.22), residues: 1460
  helix:  0.90 (0.23), residues: 479
  sheet:  1.16 (0.30), residues: 307
  loop : -0.86 (0.24), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D1112 
 HIS   0.002   0.000   HIS B1115 
 PHE   0.019   0.001   PHE B 298 
 TYR   0.018   0.001   TYR D 975 
 ARG   0.006   0.000   ARG D1081 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26223 (  490)
  hydrogen bonds       : angle       7.08813 ( 1380)
  SS BOND              : bond        0.00780 (    1)
  SS BOND              : angle       2.81024 (    2)
  covalent geometry    : bond        0.00216 (12081)
  covalent geometry    : angle       0.51457 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  315 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 312
  time to evaluate  : 1.824 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  539 TYR cc_start: 0.8055 (m-10) cc_final: 0.7815 (m-10)
REVERT: A  568 ASP cc_start: 0.6863 (m-30) cc_final: 0.6640 (m-30)
REVERT: A  593 ASP cc_start: 0.6773 (t0) cc_final: 0.6447 (t0)
REVERT: A  658 MET cc_start: 0.7475 (mmm) cc_final: 0.6620 (mmm)
REVERT: A  738 ARG cc_start: 0.7057 (ttp-110) cc_final: 0.6809 (ttp-110)
REVERT: A  810 LYS cc_start: 0.7576 (ptmt) cc_final: 0.7257 (pttt)
REVERT: B  312 ILE cc_start: 0.8341 (mt) cc_final: 0.8106 (mt)
REVERT: B  348 ASP cc_start: 0.7344 (m-30) cc_final: 0.7077 (m-30)
REVERT: B  404 LEU cc_start: 0.7897 (mt) cc_final: 0.7609 (mt)
REVERT: B  428 ASP cc_start: 0.7370 (p0) cc_final: 0.6931 (p0)
REVERT: B  528 SER cc_start: 0.8676 (t) cc_final: 0.8429 (t)
REVERT: B  618 TRP cc_start: 0.7982 (m100) cc_final: 0.7488 (m100)
REVERT: B  765 LYS cc_start: 0.7217 (ptpp) cc_final: 0.7000 (mtmm)
REVERT: B 1032 LEU cc_start: 0.8107 (mt) cc_final: 0.7907 (mt)
REVERT: B 1111 ARG cc_start: 0.7225 (ttm170) cc_final: 0.7012 (mtm-85)
REVERT: B 1193 LYS cc_start: 0.7749 (ttmt) cc_final: 0.7396 (ttmm)
  outliers start: 3
  outliers final: 0
  residues processed: 314
  average time/residue: 0.3332
  time to fit residues: 148.0410
Evaluate side-chains
  272 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 272
  time to evaluate  : 1.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 124 optimal weight:    0.8980
   chunk 112 optimal weight:    3.9990
   chunk 62 optimal weight:    0.3980
   chunk 38 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 116 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 134 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 651 HIS
B 112 HIS
B 125 GLN
B 258 ASN
B 299 GLN
B 501 HIS
B 514 HIS
B 763 ASN
B 835 GLN
B1060 ASN
B1068 GLN
B1090 ASN
** B1120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.136805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.110177 restraints weight = 18723.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3363 rms_B_bonded: 2.40
r_work: 0.3247 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  12082  Z= 0.234
  Angle     :  0.646   8.614  16389  Z= 0.342
  Chirality :  0.044   0.147   1889
  Planarity :  0.006   0.089   2070
  Dihedral  :  4.087  21.042   1595
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.13 %
    Favored  : 88.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.22), residues: 1460
  helix:  0.80 (0.23), residues: 501
  sheet:  0.76 (0.29), residues: 334
  loop : -1.05 (0.24), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 383 
 HIS   0.007   0.001   HIS B 861 
 PHE   0.032   0.002   PHE A 618 
 TYR   0.022   0.002   TYR B1028 
 ARG   0.004   0.001   ARG B 912 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05778 (  490)
  hydrogen bonds       : angle       4.95561 ( 1380)
  SS BOND              : bond        0.00434 (    1)
  SS BOND              : angle       3.68161 (    2)
  covalent geometry    : bond        0.00544 (12081)
  covalent geometry    : angle       0.64442 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 276
  time to evaluate  : 1.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  979 PHE cc_start: 0.8235 (m-10) cc_final: 0.7951 (m-10)
REVERT: A  503 SER cc_start: 0.7817 (t) cc_final: 0.7519 (m)
REVERT: A  593 ASP cc_start: 0.7785 (t0) cc_final: 0.7433 (t0)
REVERT: A  598 SER cc_start: 0.8538 (p) cc_final: 0.8190 (m)
REVERT: A  602 ILE cc_start: 0.8452 (mm) cc_final: 0.8180 (mt)
REVERT: A  658 MET cc_start: 0.8173 (mmm) cc_final: 0.7638 (mmm)
REVERT: A  738 ARG cc_start: 0.7791 (ttp-110) cc_final: 0.7436 (ttp-110)
REVERT: A  810 LYS cc_start: 0.8152 (ptmt) cc_final: 0.7754 (pttt)
REVERT: B  348 ASP cc_start: 0.8046 (m-30) cc_final: 0.7704 (m-30)
REVERT: B  428 ASP cc_start: 0.8305 (p0) cc_final: 0.8043 (p0)
REVERT: B  510 GLU cc_start: 0.7738 (tp30) cc_final: 0.7376 (tp30)
REVERT: B  582 TYR cc_start: 0.8333 (m-80) cc_final: 0.7930 (m-80)
REVERT: B  604 ARG cc_start: 0.8016 (tmt-80) cc_final: 0.7763 (tmt-80)
REVERT: B  618 TRP cc_start: 0.8108 (m100) cc_final: 0.7779 (m100)
REVERT: B  754 LYS cc_start: 0.8099 (ptmt) cc_final: 0.7887 (ptmt)
REVERT: B  805 THR cc_start: 0.8829 (t) cc_final: 0.8338 (p)
REVERT: B  810 ILE cc_start: 0.8685 (mt) cc_final: 0.8356 (tt)
REVERT: B  813 SER cc_start: 0.8408 (m) cc_final: 0.8033 (p)
REVERT: B  823 MET cc_start: 0.8447 (mmm) cc_final: 0.7915 (mpp)
REVERT: B 1193 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7813 (ttmm)
  outliers start: 23
  outliers final: 14
  residues processed: 289
  average time/residue: 0.2628
  time to fit residues: 106.7884
Evaluate side-chains
  266 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 252
  time to evaluate  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue 1039 THR
Chi-restraints excluded: chain A residue  605 HIS
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain B residue  516 CYS
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  804 CYS
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1016 LEU
Chi-restraints excluded: chain B residue 1038 THR
Chi-restraints excluded: chain B residue 1121 VAL
Chi-restraints excluded: chain B residue 1171 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 113 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 133 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
A 615 HIS
B 125 GLN
B 258 ASN
B 299 GLN
B 429 ASN
B 514 HIS
B 578 HIS
** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1060 ASN
B1120 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.135813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.108692 restraints weight = 18886.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.3343 rms_B_bonded: 2.44
r_work: 0.3224 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12082  Z= 0.205
  Angle     :  0.585   8.743  16389  Z= 0.306
  Chirality :  0.043   0.145   1889
  Planarity :  0.005   0.076   2070
  Dihedral  :  4.116  22.717   1595
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.57 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.22), residues: 1460
  helix:  0.94 (0.23), residues: 505
  sheet:  0.75 (0.29), residues: 344
  loop : -1.18 (0.24), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B1094 
 HIS   0.006   0.001   HIS A 521 
 PHE   0.030   0.002   PHE A 618 
 TYR   0.012   0.001   TYR B1028 
 ARG   0.004   0.000   ARG B1148 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05521 (  490)
  hydrogen bonds       : angle       4.70407 ( 1380)
  SS BOND              : bond        0.01199 (    1)
  SS BOND              : angle       0.88564 (    2)
  covalent geometry    : bond        0.00485 (12081)
  covalent geometry    : angle       0.58504 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 269
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  979 PHE cc_start: 0.8266 (m-10) cc_final: 0.8025 (m-10)
REVERT: A  503 SER cc_start: 0.7994 (t) cc_final: 0.7628 (m)
REVERT: A  528 GLU cc_start: 0.7785 (mp0) cc_final: 0.7403 (mp0)
REVERT: A  593 ASP cc_start: 0.7879 (t0) cc_final: 0.7560 (t0)
REVERT: A  658 MET cc_start: 0.8156 (mmm) cc_final: 0.7611 (mmm)
REVERT: A  716 THR cc_start: 0.8115 (m) cc_final: 0.7877 (m)
REVERT: A  738 ARG cc_start: 0.7707 (ttp-110) cc_final: 0.7384 (ttp-110)
REVERT: B  180 GLU cc_start: 0.7376 (mp0) cc_final: 0.7134 (mp0)
REVERT: B  348 ASP cc_start: 0.8011 (m-30) cc_final: 0.7669 (m-30)
REVERT: B  351 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7918 (mtt90)
REVERT: B  428 ASP cc_start: 0.8246 (p0) cc_final: 0.7881 (p0)
REVERT: B  510 GLU cc_start: 0.7795 (tp30) cc_final: 0.7519 (tp30)
REVERT: B  573 MET cc_start: 0.8758 (ptt) cc_final: 0.8491 (ptm)
REVERT: B  604 ARG cc_start: 0.7999 (tmt-80) cc_final: 0.7594 (tmt170)
REVERT: B  618 TRP cc_start: 0.8147 (m100) cc_final: 0.7906 (m100)
REVERT: B  754 LYS cc_start: 0.8061 (ptmt) cc_final: 0.7822 (ptmt)
REVERT: B  787 SER cc_start: 0.9037 (OUTLIER) cc_final: 0.8774 (m)
REVERT: B  805 THR cc_start: 0.8865 (t) cc_final: 0.8407 (p)
REVERT: B  810 ILE cc_start: 0.8685 (mt) cc_final: 0.8315 (tt)
REVERT: B  823 MET cc_start: 0.8355 (mmm) cc_final: 0.8121 (mmm)
REVERT: B 1058 ILE cc_start: 0.8107 (mm) cc_final: 0.7870 (mt)
REVERT: B 1177 THR cc_start: 0.8465 (m) cc_final: 0.7268 (t)
REVERT: B 1193 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7866 (ttmm)
  outliers start: 30
  outliers final: 22
  residues processed: 286
  average time/residue: 0.2628
  time to fit residues: 105.6862
Evaluate side-chains
  281 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 258
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  605 HIS
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  306 LEU
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  592 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  606 MET
Chi-restraints excluded: chain B residue  680 VAL
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  787 SER
Chi-restraints excluded: chain B residue  804 CYS
Chi-restraints excluded: chain B residue  887 LEU
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1000 CYS
Chi-restraints excluded: chain B residue 1016 LEU
Chi-restraints excluded: chain B residue 1050 ILE
Chi-restraints excluded: chain B residue 1073 ILE
Chi-restraints excluded: chain B residue 1171 ASP
Chi-restraints excluded: chain B residue 1201 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 6 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 132 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 124 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 121 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 258 ASN
B 514 HIS
B 545 ASN
B 690 HIS
** B 888 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 = 0.3736 r_free = 0.3736 target = 0.135408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.108579 restraints weight = 18690.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 2.44
r_work: 0.3218 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12082  Z= 0.175
  Angle     :  0.556  10.680  16389  Z= 0.291
  Chirality :  0.042   0.147   1889
  Planarity :  0.005   0.077   2070
  Dihedral  :  4.099  23.389   1595
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 15.31 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.22), residues: 1460
  helix:  1.02 (0.23), residues: 506
  sheet:  0.71 (0.30), residues: 335
  loop : -1.22 (0.24), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B1094 
 HIS   0.006   0.001   HIS A 521 
 PHE   0.030   0.002   PHE A 618 
 TYR   0.016   0.001   TYR B1028 
 ARG   0.003   0.000   ARG B 831 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04735 (  490)
  hydrogen bonds       : angle       4.53126 ( 1380)
  SS BOND              : bond        0.00425 (    1)
  SS BOND              : angle       2.76066 (    2)
  covalent geometry    : bond        0.00415 (12081)
  covalent geometry    : angle       0.55501 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  302 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 273
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  979 PHE cc_start: 0.8249 (m-10) cc_final: 0.8001 (m-10)
REVERT: A  503 SER cc_start: 0.8074 (t) cc_final: 0.7730 (m)
REVERT: A  528 GLU cc_start: 0.7786 (mp0) cc_final: 0.7401 (mp0)
REVERT: A  593 ASP cc_start: 0.7976 (t0) cc_final: 0.7609 (t0)
REVERT: A  658 MET cc_start: 0.8117 (mmm) cc_final: 0.7589 (mmm)
REVERT: A  738 ARG cc_start: 0.7709 (ttp-110) cc_final: 0.7403 (ttp-110)
REVERT: B  180 GLU cc_start: 0.7356 (mp0) cc_final: 0.7024 (mp0)
REVERT: B  348 ASP cc_start: 0.8002 (m-30) cc_final: 0.7682 (m-30)
REVERT: B  428 ASP cc_start: 0.8249 (p0) cc_final: 0.7904 (p0)
REVERT: B  510 GLU cc_start: 0.7760 (tp30) cc_final: 0.7497 (tp30)
REVERT: B  573 MET cc_start: 0.8710 (ptt) cc_final: 0.8449 (ptm)
REVERT: B  618 TRP cc_start: 0.8204 (m100) cc_final: 0.7748 (m100)
REVERT: B  754 LYS cc_start: 0.8050 (ptmt) cc_final: 0.7817 (ptmt)
REVERT: B  805 THR cc_start: 0.8829 (t) cc_final: 0.8334 (p)
REVERT: B  823 MET cc_start: 0.8351 (mmm) cc_final: 0.8067 (mmm)
REVERT: B 1002 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7867 (m-30)
REVERT: B 1193 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7862 (ttmm)
  outliers start: 29
  outliers final: 20
  residues processed: 289
  average time/residue: 0.2743
  time to fit residues: 108.4385
Evaluate side-chains
  290 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 269
  time to evaluate  : 1.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  605 HIS
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  260 MET
Chi-restraints excluded: chain B residue  364 CYS
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  606 MET
Chi-restraints excluded: chain B residue  680 VAL
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  804 CYS
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1002 ASP
Chi-restraints excluded: chain B residue 1016 LEU
Chi-restraints excluded: chain B residue 1050 ILE
Chi-restraints excluded: chain B residue 1104 GLU
Chi-restraints excluded: chain B residue 1142 GLU
Chi-restraints excluded: chain B residue 1171 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9990
   chunk 105 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9980
   chunk 4 optimal weight:    0.4980
   chunk 66 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 59 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 94 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 660 ASN
B 258 ASN
B 514 HIS
** B 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.135360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.108643 restraints weight = 18692.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.42
r_work: 0.3223 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7909
moved from start:          0.3385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12082  Z= 0.169
  Angle     :  0.555  12.928  16389  Z= 0.289
  Chirality :  0.042   0.148   1889
  Planarity :  0.005   0.073   2070
  Dihedral  :  4.091  22.859   1595
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 16.60 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.22), residues: 1460
  helix:  1.13 (0.23), residues: 506
  sheet:  0.69 (0.30), residues: 335
  loop : -1.24 (0.24), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B1094 
 HIS   0.004   0.001   HIS A 521 
 PHE   0.031   0.002   PHE A 618 
 TYR   0.013   0.001   TYR B1028 
 ARG   0.006   0.000   ARG A 558 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04680 (  490)
  hydrogen bonds       : angle       4.44703 ( 1380)
  SS BOND              : bond        0.00452 (    1)
  SS BOND              : angle       2.26073 (    2)
  covalent geometry    : bond        0.00401 (12081)
  covalent geometry    : angle       0.55496 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 275
  time to evaluate  : 1.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  979 PHE cc_start: 0.8243 (m-10) cc_final: 0.7975 (m-10)
REVERT: A  503 SER cc_start: 0.8166 (t) cc_final: 0.7788 (m)
REVERT: A  528 GLU cc_start: 0.7781 (mp0) cc_final: 0.7378 (mp0)
REVERT: A  593 ASP cc_start: 0.7989 (t0) cc_final: 0.7612 (t0)
REVERT: A  658 MET cc_start: 0.8128 (mmm) cc_final: 0.7556 (mmm)
REVERT: A  738 ARG cc_start: 0.7763 (ttp-110) cc_final: 0.7455 (ttp-110)
REVERT: A  739 LYS cc_start: 0.8510 (mtpp) cc_final: 0.8236 (mtpp)
REVERT: B  348 ASP cc_start: 0.7993 (m-30) cc_final: 0.7685 (m-30)
REVERT: B  510 GLU cc_start: 0.7745 (tp30) cc_final: 0.7483 (tp30)
REVERT: B  573 MET cc_start: 0.8693 (ptt) cc_final: 0.8437 (ptm)
REVERT: B  754 LYS cc_start: 0.8013 (ptmt) cc_final: 0.7800 (ptmt)
REVERT: B  805 THR cc_start: 0.8817 (t) cc_final: 0.8345 (p)
REVERT: B  823 MET cc_start: 0.8287 (mmm) cc_final: 0.8064 (mmm)
REVERT: B 1151 ASP cc_start: 0.8086 (t0) cc_final: 0.7822 (p0)
REVERT: B 1193 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7819 (ttmm)
  outliers start: 32
  outliers final: 26
  residues processed: 292
  average time/residue: 0.2778
  time to fit residues: 111.0076
Evaluate side-chains
  288 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 262
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  605 HIS
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain B residue   80 SER
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  260 MET
Chi-restraints excluded: chain B residue  364 CYS
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  606 MET
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  680 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  986 LEU
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1016 LEU
Chi-restraints excluded: chain B residue 1050 ILE
Chi-restraints excluded: chain B residue 1104 GLU
Chi-restraints excluded: chain B residue 1142 GLU
Chi-restraints excluded: chain B residue 1171 ASP
Chi-restraints excluded: chain B residue 1201 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 129 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 140 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 117 optimal weight:    0.1980
   chunk 29 optimal weight:    0.6980
   chunk 143 optimal weight:    0.9980
   chunk 88 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
D 985 ASN
A 565 GLN
** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 GLN
B 514 HIS
** B 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.135447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.108698 restraints weight = 18841.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.42
r_work: 0.3226 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3062 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12082  Z= 0.152
  Angle     :  0.544  11.625  16389  Z= 0.282
  Chirality :  0.042   0.142   1889
  Planarity :  0.004   0.072   2070
  Dihedral  :  4.025  22.560   1595
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 17.36 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.22), residues: 1460
  helix:  1.23 (0.23), residues: 504
  sheet:  0.64 (0.30), residues: 333
  loop : -1.25 (0.24), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1094 
 HIS   0.004   0.001   HIS A 521 
 PHE   0.033   0.001   PHE A 618 
 TYR   0.012   0.001   TYR B1028 
 ARG   0.005   0.000   ARG B 912 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04324 (  490)
  hydrogen bonds       : angle       4.33471 ( 1380)
  SS BOND              : bond        0.00384 (    1)
  SS BOND              : angle       2.21581 (    2)
  covalent geometry    : bond        0.00361 (12081)
  covalent geometry    : angle       0.54348 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  305 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 269
  time to evaluate  : 1.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  979 PHE cc_start: 0.8238 (m-10) cc_final: 0.7959 (m-10)
REVERT: A  503 SER cc_start: 0.8233 (t) cc_final: 0.7837 (m)
REVERT: A  528 GLU cc_start: 0.7792 (mp0) cc_final: 0.7395 (mp0)
REVERT: A  593 ASP cc_start: 0.8001 (t0) cc_final: 0.7618 (t0)
REVERT: A  634 MET cc_start: 0.8413 (mtm) cc_final: 0.8212 (mtp)
REVERT: A  658 MET cc_start: 0.8126 (mmm) cc_final: 0.7581 (mmm)
REVERT: A  738 ARG cc_start: 0.7785 (ttp-110) cc_final: 0.7466 (ttp-110)
REVERT: B  180 GLU cc_start: 0.7231 (mp0) cc_final: 0.6822 (mp0)
REVERT: B  348 ASP cc_start: 0.8001 (m-30) cc_final: 0.7676 (m-30)
REVERT: B  510 GLU cc_start: 0.7739 (tp30) cc_final: 0.7484 (tp30)
REVERT: B  573 MET cc_start: 0.8629 (ptt) cc_final: 0.8377 (ptm)
REVERT: B 1002 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7841 (m-30)
REVERT: B 1193 LYS cc_start: 0.8121 (ttmt) cc_final: 0.7817 (ttmm)
  outliers start: 36
  outliers final: 30
  residues processed: 287
  average time/residue: 0.2856
  time to fit residues: 112.1752
Evaluate side-chains
  295 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 264
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue 1050 ILE
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  605 HIS
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  260 MET
Chi-restraints excluded: chain B residue  364 CYS
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  606 MET
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  680 VAL
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1002 ASP
Chi-restraints excluded: chain B residue 1016 LEU
Chi-restraints excluded: chain B residue 1050 ILE
Chi-restraints excluded: chain B residue 1067 VAL
Chi-restraints excluded: chain B residue 1073 ILE
Chi-restraints excluded: chain B residue 1104 GLU
Chi-restraints excluded: chain B residue 1113 VAL
Chi-restraints excluded: chain B residue 1142 GLU
Chi-restraints excluded: chain B residue 1171 ASP
Chi-restraints excluded: chain B residue 1201 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 119 optimal weight:    0.0870
   chunk 132 optimal weight:    0.5980
   chunk 97 optimal weight:    0.9980
   chunk 146 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:    0.2980
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 125 GLN
B 514 HIS
** B 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.135607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.108920 restraints weight = 18813.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.44
r_work: 0.3231 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12082  Z= 0.127
  Angle     :  0.529  14.281  16389  Z= 0.273
  Chirality :  0.041   0.142   1889
  Planarity :  0.004   0.070   2070
  Dihedral  :  3.939  21.959   1595
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 18.05 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.22), residues: 1460
  helix:  1.31 (0.23), residues: 504
  sheet:  0.74 (0.30), residues: 321
  loop : -1.24 (0.24), residues: 635

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1094 
 HIS   0.003   0.001   HIS B 578 
 PHE   0.034   0.001   PHE A 618 
 TYR   0.011   0.001   TYR B1028 
 ARG   0.004   0.000   ARG A 558 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03960 (  490)
  hydrogen bonds       : angle       4.23235 ( 1380)
  SS BOND              : bond        0.00306 (    1)
  SS BOND              : angle       1.94809 (    2)
  covalent geometry    : bond        0.00302 (12081)
  covalent geometry    : angle       0.52877 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 270
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  979 PHE cc_start: 0.8261 (m-10) cc_final: 0.7964 (m-10)
REVERT: A  503 SER cc_start: 0.8255 (t) cc_final: 0.7861 (m)
REVERT: A  528 GLU cc_start: 0.7803 (mp0) cc_final: 0.7406 (mp0)
REVERT: A  559 LYS cc_start: 0.8159 (mtpp) cc_final: 0.7891 (mtpp)
REVERT: A  593 ASP cc_start: 0.8011 (t0) cc_final: 0.7629 (t0)
REVERT: A  658 MET cc_start: 0.8092 (mmm) cc_final: 0.7618 (mmm)
REVERT: A  738 ARG cc_start: 0.7761 (ttp-110) cc_final: 0.7433 (ttp-110)
REVERT: B  348 ASP cc_start: 0.7980 (m-30) cc_final: 0.7646 (m-30)
REVERT: B  510 GLU cc_start: 0.7705 (tp30) cc_final: 0.7446 (tp30)
REVERT: B  573 MET cc_start: 0.8619 (ptt) cc_final: 0.8372 (ptm)
REVERT: B  831 ARG cc_start: 0.8048 (mtp-110) cc_final: 0.7697 (mtm110)
REVERT: B 1019 GLU cc_start: 0.7702 (mt-10) cc_final: 0.7433 (mm-30)
REVERT: B 1193 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7810 (ttmm)
  outliers start: 36
  outliers final: 28
  residues processed: 290
  average time/residue: 0.2815
  time to fit residues: 112.5900
Evaluate side-chains
  289 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 261
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  605 HIS
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  260 MET
Chi-restraints excluded: chain B residue  364 CYS
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  606 MET
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  680 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1050 ILE
Chi-restraints excluded: chain B residue 1073 ILE
Chi-restraints excluded: chain B residue 1104 GLU
Chi-restraints excluded: chain B residue 1113 VAL
Chi-restraints excluded: chain B residue 1142 GLU
Chi-restraints excluded: chain B residue 1201 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 77 optimal weight:    1.9990
   chunk 97 optimal weight:    0.1980
   chunk 34 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 64 optimal weight:    0.3980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 768 GLN
B 125 GLN
B 514 HIS
** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 578 HIS
** B 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1068 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.135684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.109063 restraints weight = 19001.415|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.43
r_work: 0.3228 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.78 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12082  Z= 0.126
  Angle     :  0.534  13.694  16389  Z= 0.275
  Chirality :  0.041   0.142   1889
  Planarity :  0.004   0.069   2070
  Dihedral  :  3.894  21.760   1595
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 18.81 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.22), residues: 1460
  helix:  1.38 (0.23), residues: 499
  sheet:  0.73 (0.31), residues: 322
  loop : -1.24 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1094 
 HIS   0.003   0.001   HIS B 578 
 PHE   0.031   0.001   PHE A 618 
 TYR   0.010   0.001   TYR B1028 
 ARG   0.005   0.000   ARG B 912 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03832 (  490)
  hydrogen bonds       : angle       4.17545 ( 1380)
  SS BOND              : bond        0.00289 (    1)
  SS BOND              : angle       1.85230 (    2)
  covalent geometry    : bond        0.00299 (12081)
  covalent geometry    : angle       0.53334 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 266
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  979 PHE cc_start: 0.8260 (m-10) cc_final: 0.7985 (m-10)
REVERT: A  406 MET cc_start: 0.5922 (mmm) cc_final: 0.5239 (mmt)
REVERT: A  503 SER cc_start: 0.8271 (t) cc_final: 0.7868 (m)
REVERT: A  528 GLU cc_start: 0.7829 (mp0) cc_final: 0.7424 (mp0)
REVERT: A  559 LYS cc_start: 0.8160 (mtpp) cc_final: 0.7908 (mtpp)
REVERT: A  593 ASP cc_start: 0.8035 (t0) cc_final: 0.7656 (t0)
REVERT: A  634 MET cc_start: 0.8694 (mtp) cc_final: 0.8394 (mtp)
REVERT: A  658 MET cc_start: 0.8127 (mmm) cc_final: 0.7661 (mmm)
REVERT: A  738 ARG cc_start: 0.7726 (ttp-110) cc_final: 0.7399 (ttp-110)
REVERT: B  348 ASP cc_start: 0.7995 (m-30) cc_final: 0.7660 (m-30)
REVERT: B  357 ARG cc_start: 0.8415 (ptp-110) cc_final: 0.8178 (ptp90)
REVERT: B  428 ASP cc_start: 0.8324 (p0) cc_final: 0.7992 (p0)
REVERT: B  510 GLU cc_start: 0.7745 (tp30) cc_final: 0.7459 (tp30)
REVERT: B  573 MET cc_start: 0.8622 (ptt) cc_final: 0.8371 (ptm)
REVERT: B 1002 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7846 (m-30)
REVERT: B 1019 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7399 (mm-30)
REVERT: B 1193 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7794 (ttmm)
  outliers start: 27
  outliers final: 22
  residues processed: 280
  average time/residue: 0.2714
  time to fit residues: 103.8224
Evaluate side-chains
  287 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 264
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue 1050 ILE
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  606 MET
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  680 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue 1002 ASP
Chi-restraints excluded: chain B residue 1050 ILE
Chi-restraints excluded: chain B residue 1104 GLU
Chi-restraints excluded: chain B residue 1113 VAL
Chi-restraints excluded: chain B residue 1142 GLU
Chi-restraints excluded: chain B residue 1201 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 126 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   chunk 115 optimal weight:    0.5980
   chunk 24 optimal weight:    0.3980
   chunk 17 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9980
   chunk 14 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 768 GLN
B 125 GLN
B 514 HIS
** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1060 ASN
B1068 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.134871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.108494 restraints weight = 18833.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.42
r_work: 0.3216 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.3772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  12082  Z= 0.163
  Angle     :  0.561  13.412  16389  Z= 0.290
  Chirality :  0.042   0.147   1889
  Planarity :  0.004   0.070   2070
  Dihedral  :  4.019  21.663   1595
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 19.42 %
    Favored  : 78.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.22), residues: 1460
  helix:  1.40 (0.24), residues: 499
  sheet:  0.71 (0.31), residues: 322
  loop : -1.28 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B1094 
 HIS   0.004   0.001   HIS B 578 
 PHE   0.029   0.002   PHE A 618 
 TYR   0.011   0.001   TYR B1028 
 ARG   0.006   0.000   ARG B 912 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04361 (  490)
  hydrogen bonds       : angle       4.26530 ( 1380)
  SS BOND              : bond        0.00425 (    1)
  SS BOND              : angle       2.15633 (    2)
  covalent geometry    : bond        0.00392 (12081)
  covalent geometry    : angle       0.56059 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 266
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  979 PHE cc_start: 0.8250 (m-10) cc_final: 0.7985 (m-10)
REVERT: A  406 MET cc_start: 0.5846 (mmm) cc_final: 0.5175 (mmt)
REVERT: A  503 SER cc_start: 0.8296 (t) cc_final: 0.7905 (m)
REVERT: A  528 GLU cc_start: 0.7832 (mp0) cc_final: 0.7393 (mp0)
REVERT: A  559 LYS cc_start: 0.8183 (mtpp) cc_final: 0.7924 (mtpp)
REVERT: A  593 ASP cc_start: 0.7992 (t0) cc_final: 0.7630 (t0)
REVERT: A  634 MET cc_start: 0.8693 (mtp) cc_final: 0.8364 (mtp)
REVERT: A  658 MET cc_start: 0.8169 (mmm) cc_final: 0.7635 (mmm)
REVERT: A  738 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7350 (ttp-110)
REVERT: A  744 ILE cc_start: 0.7531 (mm) cc_final: 0.7288 (mm)
REVERT: B  348 ASP cc_start: 0.8028 (m-30) cc_final: 0.7683 (m-30)
REVERT: B  428 ASP cc_start: 0.8327 (p0) cc_final: 0.7995 (p0)
REVERT: B  510 GLU cc_start: 0.7733 (tp30) cc_final: 0.7469 (tp30)
REVERT: B  573 MET cc_start: 0.8621 (ptt) cc_final: 0.8368 (ptm)
REVERT: B  831 ARG cc_start: 0.8078 (mtp-110) cc_final: 0.7755 (mtm110)
REVERT: B 1019 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7454 (mm-30)
REVERT: B 1177 THR cc_start: 0.8425 (m) cc_final: 0.7241 (t)
REVERT: B 1193 LYS cc_start: 0.8128 (ttmt) cc_final: 0.7833 (ttmm)
  outliers start: 29
  outliers final: 25
  residues processed: 282
  average time/residue: 0.2802
  time to fit residues: 108.3068
Evaluate side-chains
  288 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 263
  time to evaluate  : 1.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue 1050 ILE
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  364 CYS
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  552 LEU
Chi-restraints excluded: chain B residue  572 GLU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  606 MET
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  680 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1050 ILE
Chi-restraints excluded: chain B residue 1104 GLU
Chi-restraints excluded: chain B residue 1113 VAL
Chi-restraints excluded: chain B residue 1142 GLU
Chi-restraints excluded: chain B residue 1201 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 116 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0970
   chunk 15 optimal weight:    0.9980
   chunk 136 optimal weight:    1.9990
   chunk 121 optimal weight:    0.3980
   chunk 131 optimal weight:    0.5980
   chunk 120 optimal weight:    0.5980
   chunk 142 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 20 optimal weight:   10.0000
   chunk 125 optimal weight:    0.4980
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 768 GLN
B 125 GLN
B 514 HIS
** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 578 HIS
** B 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 835 GLN
** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1060 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.135664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.109324 restraints weight = 18745.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.41
r_work: 0.3232 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12082  Z= 0.120
  Angle     :  0.534  13.087  16389  Z= 0.276
  Chirality :  0.041   0.147   1889
  Planarity :  0.004   0.068   2070
  Dihedral  :  3.896  21.987   1595
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 19.80 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.23), residues: 1460
  helix:  1.47 (0.24), residues: 498
  sheet:  0.71 (0.31), residues: 322
  loop : -1.23 (0.24), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 153 
 HIS   0.003   0.001   HIS B 578 
 PHE   0.030   0.001   PHE A 618 
 TYR   0.010   0.001   TYR B1028 
 ARG   0.008   0.000   ARG B 351 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03686 (  490)
  hydrogen bonds       : angle       4.13078 ( 1380)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       1.79098 (    2)
  covalent geometry    : bond        0.00284 (12081)
  covalent geometry    : angle       0.53358 (16387)

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

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

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2920 Ramachandran restraints generated.
    1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 266
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  979 PHE cc_start: 0.8248 (m-10) cc_final: 0.7982 (m-10)
REVERT: A  406 MET cc_start: 0.5927 (mmm) cc_final: 0.5215 (mmt)
REVERT: A  503 SER cc_start: 0.8259 (t) cc_final: 0.7857 (m)
REVERT: A  528 GLU cc_start: 0.7808 (mp0) cc_final: 0.7452 (mp0)
REVERT: A  559 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7895 (mtpp)
REVERT: A  593 ASP cc_start: 0.8011 (t0) cc_final: 0.7638 (t0)
REVERT: A  634 MET cc_start: 0.8676 (mtp) cc_final: 0.8384 (mtp)
REVERT: A  658 MET cc_start: 0.8127 (mmm) cc_final: 0.7671 (mmm)
REVERT: A  738 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.7344 (ttp-110)
REVERT: A  744 ILE cc_start: 0.7507 (mm) cc_final: 0.7273 (mm)
REVERT: B  180 GLU cc_start: 0.7422 (mp0) cc_final: 0.7131 (mp0)
REVERT: B  348 ASP cc_start: 0.8009 (m-30) cc_final: 0.7656 (m-30)
REVERT: B  357 ARG cc_start: 0.8425 (ptp-110) cc_final: 0.8170 (ptp90)
REVERT: B  428 ASP cc_start: 0.8345 (p0) cc_final: 0.8009 (p0)
REVERT: B  510 GLU cc_start: 0.7737 (tp30) cc_final: 0.7457 (tp30)
REVERT: B  573 MET cc_start: 0.8594 (ptt) cc_final: 0.8346 (ptm)
REVERT: B 1019 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7406 (mm-30)
REVERT: B 1177 THR cc_start: 0.8382 (m) cc_final: 0.7103 (t)
REVERT: B 1193 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7834 (ttmm)
  outliers start: 26
  outliers final: 24
  residues processed: 282
  average time/residue: 0.2758
  time to fit residues: 106.8032
Evaluate side-chains
  287 residues out of total 1313 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 263
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue 1050 ILE
Chi-restraints excluded: chain A residue  602 ILE
Chi-restraints excluded: chain A residue  605 HIS
Chi-restraints excluded: chain A residue  622 GLU
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain B residue   90 ASP
Chi-restraints excluded: chain B residue  119 VAL
Chi-restraints excluded: chain B residue  165 SER
Chi-restraints excluded: chain B residue  364 CYS
Chi-restraints excluded: chain B residue  526 LEU
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  606 MET
Chi-restraints excluded: chain B residue  619 SER
Chi-restraints excluded: chain B residue  680 VAL
Chi-restraints excluded: chain B residue  728 MET
Chi-restraints excluded: chain B residue  755 ILE
Chi-restraints excluded: chain B residue  766 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  989 VAL
Chi-restraints excluded: chain B residue 1050 ILE
Chi-restraints excluded: chain B residue 1060 ASN
Chi-restraints excluded: chain B residue 1113 VAL
Chi-restraints excluded: chain B residue 1142 GLU
Chi-restraints excluded: chain B residue 1201 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 106 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 120 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 130 optimal weight:    0.8980
   chunk 105 optimal weight:    0.4980
   chunk 68 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0670
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 565 GLN
** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 768 GLN
B 125 GLN
B 514 HIS
** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 578 HIS
** B 678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 835 GLN
** B 888 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1060 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.134568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108069 restraints weight = 18764.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.42
r_work: 0.3222 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12082  Z= 0.145
  Angle     :  0.553  13.040  16389  Z= 0.285
  Chirality :  0.041   0.145   1889
  Planarity :  0.004   0.070   2070
  Dihedral  :  3.930  21.622   1595
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 19.57 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.22), residues: 1460
  helix:  1.43 (0.23), residues: 498
  sheet:  0.69 (0.31), residues: 323
  loop : -1.24 (0.24), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B1094 
 HIS   0.004   0.001   HIS B 578 
 PHE   0.029   0.001   PHE A 618 
 TYR   0.010   0.001   TYR B1028 
 ARG   0.008   0.000   ARG B 351 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04012 (  490)
  hydrogen bonds       : angle       4.18918 ( 1380)
  SS BOND              : bond        0.00359 (    1)
  SS BOND              : angle       1.98446 (    2)
  covalent geometry    : bond        0.00349 (12081)
  covalent geometry    : angle       0.55284 (16387)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7274.16 seconds
wall clock time: 125 minutes 42.86 seconds (7542.86 seconds total)