Starting phenix.real_space_refine
on Wed Sep 17 23:44:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9asp_43822/09_2025/9asp_43822.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9asp_43822/09_2025/9asp_43822.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9asp_43822/09_2025/9asp_43822.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9asp_43822/09_2025/9asp_43822.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9asp_43822/09_2025/9asp_43822.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9asp_43822/09_2025/9asp_43822.map"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      2      6.06       5
     P      96      5.49       5
     S      64      5.16       5
     C    7386      2.51       5
     N    2145      2.21       5
     O    2532      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12227
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7468
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 914, 7468
          Classifications: {'peptide': 914}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 52, 'TRANS': 861}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 1990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1990
          Classifications: {'peptide': 250}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 10, 'TRANS': 239}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "C"
      Number of atoms: 729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 729
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 4, 'TRANS': 87}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 2035
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 2035
          Classifications: {'RNA': 96}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 40, 'rna3p_pyr': 42}
          Link IDs: {'rna2p': 13, 'rna3p': 82}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 1, ' ZN': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    955  SG  CYS A 561      42.918  81.838 148.452  1.00172.12           S
  ATOM   1913  SG  CYS A 676      45.995  79.463 148.191  1.00178.36           S
  ATOM    763  SG  CYS A 536      61.773  62.441 134.035  1.00181.72           S
  ATOM    778  SG  CYS A 538      62.519  61.043 130.484  1.00190.39           S

  Time building chain proxies: 2.59, per 1000 atoms: 0.21
  Number of scatterers: 12227
  At special positions: 0
  Unit cell: (90.2, 103.4, 194.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     Ca      2     19.99
     S      64     16.00
     P      96     15.00
     O    2532      8.00
     N    2145      7.00
     C    7386      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 454.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1401 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 609 "
        pdb="ZN    ZN A1401 " - pdb=" NE2 HIS A 680 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 676 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A 561 "
      pdb="  ZN A1402 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A1026 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A 549 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 536 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A 538 "
      Number of angles added : 4


  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2386

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 10 sheets defined
      53.7% alpha, 10.9% beta
      32 base pairs and 45 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 439 through 452
      removed outlier: 4.631A  pdb=" N   ASP A 446 " --> pdb=" O   ARG A 442 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   LYS A 447 " --> pdb=" O   ASP A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 462
      removed outlier: 3.721A  pdb=" N   ALA A 462 " --> pdb=" O   LYS A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 512
    Processing helix  chain 'A' and resid 541 through 545
      removed outlier: 3.639A  pdb=" N   THR A 545 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 655
    Processing helix  chain 'A' and resid 698 through 709
      removed outlier: 3.625A  pdb=" N   ILE A 702 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 725
    Processing helix  chain 'A' and resid 726 through 737
      removed outlier: 3.816A  pdb=" N   CYS A 737 " --> pdb=" O   TYR A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 783 through 786
    Processing helix  chain 'A' and resid 787 through 806
      removed outlier: 3.527A  pdb=" N   GLN A 791 " --> pdb=" O   ASP A 787 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU A 800 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   ASN A 806 " --> pdb=" O   HIS A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 812 through 830
      removed outlier: 4.076A  pdb=" N   GLN A 816 " --> pdb=" O   GLN A 812 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LYS A 817 " --> pdb=" O   THR A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 861
      removed outlier: 3.975A  pdb=" N   CYS A 857 " --> pdb=" O   ARG A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 884
      removed outlier: 3.714A  pdb=" N   LEU A 866 " --> pdb=" O   MET A 862 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   MET A 877 " --> pdb=" O   HIS A 873 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   HIS A 878 " --> pdb=" O   GLN A 874 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   LEU A 879 " --> pdb=" O   CYS A 875 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 897
      removed outlier: 3.769A  pdb=" N   MET A 897 " --> pdb=" O   LEU A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 921
      removed outlier: 3.526A  pdb=" N   ALA A 913 " --> pdb=" O   ASN A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 934
      removed outlier: 3.906A  pdb=" N   VAL A 932 " --> pdb=" O   ASP A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 941 through 950
      removed outlier: 3.647A  pdb=" N   ILE A 946 " --> pdb=" O   ILE A 942 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ASN A 947 " --> pdb=" O   ASN A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 988
      removed outlier: 4.009A  pdb=" N   PHE A 970 " --> pdb=" O   GLU A 966 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LEU A 971 " --> pdb=" O   ARG A 967 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   ALA A 974 " --> pdb=" O   PHE A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1005
      removed outlier: 3.617A  pdb=" N   GLN A1005 " --> pdb=" O   THR A1001 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1005 through 1014
    Processing helix  chain 'A' and resid 1015 through 1016
      No H-bonds generated for 'chain 'A' and resid 1015 through 1016'
    Processing helix  chain 'A' and resid 1017 through 1021
    Processing helix  chain 'A' and resid 1027 through 1031
      removed outlier: 3.734A  pdb=" N   LEU A1030 " --> pdb=" O   GLY A1027 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   CYS A1031 " --> pdb=" O   PRO A1028 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1027 through 1031'
    Processing helix  chain 'A' and resid 1032 through 1055
    Processing helix  chain 'A' and resid 1056 through 1069
      removed outlier: 3.997A  pdb=" N   ALA A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU A1067 " --> pdb=" O   LEU A1063 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   PHE A1069 " --> pdb=" O   GLY A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1079
    Processing helix  chain 'A' and resid 1084 through 1090
      removed outlier: 4.094A  pdb=" N   GLU A1090 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1099
      removed outlier: 3.548A  pdb=" N   LEU A1097 " --> pdb=" O   ASP A1094 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   GLU A1099 " --> pdb=" O   GLN A1096 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1115
      removed outlier: 3.608A  pdb=" N   GLN A1105 " --> pdb=" O   SER A1101 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   GLU A1109 " --> pdb=" O   GLN A1105 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE A1110 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1129
      removed outlier: 3.978A  pdb=" N   LEU A1124 " --> pdb=" O   HIS A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1166
      removed outlier: 3.520A  pdb=" N   GLU A1147 " --> pdb=" O   ASN A1143 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   SER A1152 " --> pdb=" O   PHE A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1182
      removed outlier: 3.779A  pdb=" N   LEU A1176 " --> pdb=" O   GLY A1172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1183 through 1194
    Processing helix  chain 'A' and resid 1203 through 1208
      removed outlier: 4.184A  pdb=" N   LYS A1207 " --> pdb=" O   ASN A1203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1232
    Processing helix  chain 'A' and resid 1233 through 1245
      removed outlier: 4.529A  pdb=" N   VAL A1237 " --> pdb=" O   ASP A1233 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   HIS A1238 " --> pdb=" O   LEU A1234 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL A1243 " --> pdb=" O   THR A1239 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   CYS A1244 " --> pdb=" O   PHE A1240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1255
      removed outlier: 3.855A  pdb=" N   PHE A1252 " --> pdb=" O   ARG A1248 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE A1253 " --> pdb=" O   LEU A1249 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A1254 " --> pdb=" O   LYS A1250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1271
      removed outlier: 3.698A  pdb=" N   THR A1271 " --> pdb=" O   GLN A1267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1316 through 1332
      removed outlier: 3.766A  pdb=" N   GLU A1330 " --> pdb=" O   MET A1326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1334 through 1348
      removed outlier: 3.681A  pdb=" N   ALA A1338 " --> pdb=" O   PHE A1334 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LYS A1347 " --> pdb=" O   PHE A1343 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TYR A1348 " --> pdb=" O   ILE A1344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1352 through 1356
      removed outlier: 3.518A  pdb=" N   ARG A1356 " --> pdb=" O   LYS A1353 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 511 through 524
    Processing helix  chain 'B' and resid 560 through 577
      removed outlier: 3.806A  pdb=" N   GLU B 574 " --> pdb=" O   ARG B 570 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE B 575 " --> pdb=" O   ALA B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 591 through 601
    Processing helix  chain 'B' and resid 607 through 616
      removed outlier: 3.645A  pdb=" N   LEU B 611 " --> pdb=" O   ARG B 607 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR B 612 " --> pdb=" O   VAL B 608 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 619 through 630
      removed outlier: 3.622A  pdb=" N   ILE B 623 " --> pdb=" O   SER B 619 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU B 624 " --> pdb=" O   PRO B 620 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 685
      removed outlier: 4.379A  pdb=" N   GLN B 674 " --> pdb=" O   ARG B 670 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LYS B 679 " --> pdb=" O   LEU B 675 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE B 680 " --> pdb=" O   ALA B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 708
      removed outlier: 4.155A  pdb=" N   ARG B 696 " --> pdb=" O   GLY B 692 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   MET B 697 " --> pdb=" O   SER B 693 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   TYR B 698 " --> pdb=" O   LEU B 694 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   GLU B 701 " --> pdb=" O   MET B 697 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   SER B 702 " --> pdb=" O   TYR B 698 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   VAL B 706 " --> pdb=" O   SER B 702 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN B 708 " --> pdb=" O   LYS B 704 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 711 through 721
      removed outlier: 4.031A  pdb=" N   VAL B 715 " --> pdb=" O   SER B 711 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU B 718 " --> pdb=" O   SER B 714 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   GLN B 719 " --> pdb=" O   VAL B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 749
      removed outlier: 3.575A  pdb=" N   LEU B 742 " --> pdb=" O   GLU B 738 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU B 748 " --> pdb=" O   GLU B 744 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 511 through 521
      removed outlier: 3.587A  pdb=" N   TYR C 519 " --> pdb=" O   ILE C 515 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   MET C 520 " --> pdb=" O   LEU C 516 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLN C 521 " --> pdb=" O   HIS C 517 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 560 through 577
      removed outlier: 3.553A  pdb=" N   LYS C 565 " --> pdb=" O   LYS C 561 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ASN C 566 " --> pdb=" O   LYS C 562 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ARG C 570 " --> pdb=" O   ASN C 566 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   THR C 572 " --> pdb=" O   ALA C 568 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   LEU C 573 " --> pdb=" O   ALA C 569 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLU C 574 " --> pdb=" O   ARG C 570 " (cutoff:3.500A)
      removed outlier: 4.653A  pdb=" N   ILE C 575 " --> pdb=" O   ALA C 571 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU C 576 " --> pdb=" O   THR C 572 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 728 through 749
      removed outlier: 3.794A  pdb=" N   LEU C 732 " --> pdb=" O   ASN C 728 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 415
      removed outlier: 3.665A  pdb=" N   ARG A 684 " --> pdb=" O   GLY A 603 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   GLY A 603 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   VAL A 686 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 9.192A  pdb=" N   PHE A 688 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
      removed outlier: 9.656A  pdb=" N   TYR A 599 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 608 " --> pdb=" O   PHE A 572 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 415
      removed outlier: 3.665A  pdb=" N   ARG A 684 " --> pdb=" O   GLY A 603 " (cutoff:3.500A)
      removed outlier: 5.015A  pdb=" N   GLY A 603 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   VAL A 686 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 9.192A  pdb=" N   PHE A 688 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
      removed outlier: 9.656A  pdb=" N   TYR A 599 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 423
    Processing sheet with id=AA4, first strand: chain 'A' and resid 576 through 578
      removed outlier: 4.186A  pdb=" N   CYS A 618 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 751 through 753
      removed outlier: 4.539A  pdb=" N   ILE A 741 " --> pdb=" O   THR A 850 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   THR A 850 " --> pdb=" O   ILE A 741 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 771 through 777
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1283 through 1290
      removed outlier: 3.574A  pdb=" N   ALA A1301 " --> pdb=" O   LYS A1285 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   THR A1299 " --> pdb=" O   LEU A1287 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   THR A1289 " --> pdb=" O   THR A1297 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   THR A1297 " --> pdb=" O   THR A1289 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   TYR A1298 " --> pdb=" O   LYS A1313 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   LYS A1313 " --> pdb=" O   TYR A1298 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL A1300 " --> pdb=" O   CYS A1311 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   CYS A1311 " --> pdb=" O   VAL A1300 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   VAL A1302 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 495 through 496
    Processing sheet with id=AA9, first strand: chain 'B' and resid 530 through 534
      removed outlier: 7.255A  pdb=" N   ALA B 544 " --> pdb=" O   SER B 555 " (cutoff:3.500A)
      removed outlier: 5.074A  pdb=" N   SER B 555 " --> pdb=" O   ALA B 544 " (cutoff:3.500A)
      removed outlier: 7.220A  pdb=" N   VAL B 546 " --> pdb=" O   TYR B 553 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TYR B 553 " --> pdb=" O   VAL B 546 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 639 through 644
      removed outlier: 3.613A  pdb=" N   SER B 651 " --> pdb=" O   CYS B 666 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   MET B 655 " --> pdb=" O   VAL B 662 " (cutoff:3.500A)

    449 hydrogen bonds defined for protein.
    1293 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      74 hydrogen bonds
      128 hydrogen bond angles
      0 basepair planarities
      32 basepair parallelities
      45 stacking parallelities
  Total time for adding SS restraints: 2.40

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3662
        1.34 -     1.46: 3270
        1.46 -     1.58: 5471
        1.58 -     1.71: 190
        1.71 -     1.83: 101
  Bond restraints: 12694
  Sorted by residual:
  bond pdb=" C   PHE A1166 "
       pdb=" N   PRO A1167 "
    ideal  model  delta    sigma   weight residual
    1.331  1.319  0.012 7.90e-03 1.60e+04 2.35e+00
  bond pdb=" C3'   A E  73 "
       pdb=" O3'   A E  73 "
    ideal  model  delta    sigma   weight residual
    1.427  1.444 -0.017 1.50e-02 4.44e+03 1.29e+00
  bond pdb=" CB  ILE A1153 "
       pdb=" CG2 ILE A1153 "
    ideal  model  delta    sigma   weight residual
    1.521  1.487  0.034 3.30e-02 9.18e+02 1.07e+00
  bond pdb=" CB  TRP A 794 "
       pdb=" CG  TRP A 794 "
    ideal  model  delta    sigma   weight residual
    1.498  1.466  0.032 3.10e-02 1.04e+03 1.04e+00
  bond pdb=" CG  MET A 935 "
       pdb=" SD  MET A 935 "
    ideal  model  delta    sigma   weight residual
    1.803  1.828 -0.025 2.50e-02 1.60e+03 1.01e+00
  ... (remaining 12689 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.66: 17171
        1.66 -     3.32: 365
        3.32 -     4.98: 48
        4.98 -     6.64: 10
        6.64 -     8.30: 7
  Bond angle restraints: 17601
  Sorted by residual:
  angle pdb=" C3'   A E  73 "
        pdb=" O3'   A E  73 "
        pdb=" P     A E  74 "
      ideal   model   delta    sigma   weight residual
     120.20  124.92   -4.72 1.50e+00 4.44e-01 9.90e+00
  angle pdb=" CA  MET B 634 "
        pdb=" CB  MET B 634 "
        pdb=" CG  MET B 634 "
      ideal   model   delta    sigma   weight residual
     114.10  120.06   -5.96 2.00e+00 2.50e-01 8.87e+00
  angle pdb=" N   ARG A1208 "
        pdb=" CA  ARG A1208 "
        pdb=" C   ARG A1208 "
      ideal   model   delta    sigma   weight residual
     108.13  110.74   -2.61 9.00e-01 1.23e+00 8.38e+00
  angle pdb=" N   GLY A 692 "
        pdb=" CA  GLY A 692 "
        pdb=" C   GLY A 692 "
      ideal   model   delta    sigma   weight residual
     114.48  111.15    3.33 1.19e+00 7.06e-01 7.83e+00
  angle pdb=" CB  MET B 634 "
        pdb=" CG  MET B 634 "
        pdb=" SD  MET B 634 "
      ideal   model   delta    sigma   weight residual
     112.70  121.00   -8.30 3.00e+00 1.11e-01 7.65e+00
  ... (remaining 17596 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.22: 7391
       35.22 -    70.43: 403
       70.43 -   105.65: 35
      105.65 -   140.86: 1
      140.86 -   176.08: 2
  Dihedral angle restraints: 7832
    sinusoidal: 4151
      harmonic: 3681
  Sorted by residual:
  dihedral pdb=" O4'   U E  72 "
           pdb=" C1'   U E  72 "
           pdb=" N1    U E  72 "
           pdb=" C2    U E  72 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.08 -176.08     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U E  47 "
           pdb=" C1'   U E  47 "
           pdb=" N1    U E  47 "
           pdb=" C2    U E  47 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -61.37  -66.63     1      1.70e+01 3.46e-03 2.00e+01
  dihedral pdb=" C4'   A E  73 "
           pdb=" C3'   A E  73 "
           pdb=" O3'   A E  73 "
           pdb=" P     A E  74 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -110.00   53.35 -163.35     1      3.50e+01 8.16e-04 1.53e+01
  ... (remaining 7829 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1378
       0.032 -    0.064: 424
       0.064 -    0.095: 141
       0.095 -    0.127: 48
       0.127 -    0.159: 9
  Chirality restraints: 2000
  Sorted by residual:
  chirality pdb=" C3'   A E  73 "
            pdb=" C4'   A E  73 "
            pdb=" O3'   A E  73 "
            pdb=" C2'   A E  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.59   -0.16 2.00e-01 2.50e+01 6.33e-01
  chirality pdb=" CA  SER A 579 "
            pdb=" N   SER A 579 "
            pdb=" C   SER A 579 "
            pdb=" CB  SER A 579 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.17e-01
  chirality pdb=" CA  ILE A 741 "
            pdb=" N   ILE A 741 "
            pdb=" C   ILE A 741 "
            pdb=" CB  ILE A 741 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.73e-01
  ... (remaining 1997 not shown)

  Planarity restraints: 1918
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A1027 "    0.035 5.00e-02 4.00e+02   5.30e-02 4.49e+00
        pdb=" N   PRO A1028 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO A1028 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A1028 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 725 "   -0.018 2.00e-02 2.50e+03   1.33e-02 4.45e+00
        pdb=" CG  TRP A 725 "    0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 725 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 725 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 725 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 725 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 725 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 725 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 725 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 725 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A1246 "    0.031 5.00e-02 4.00e+02   4.63e-02 3.43e+00
        pdb=" N   PRO A1247 "   -0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO A1247 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1247 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1915 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1234
        2.74 -     3.28: 11979
        3.28 -     3.82: 20338
        3.82 -     4.36: 23070
        4.36 -     4.90: 37377
  Nonbonded interactions: 93998
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 561 "
            pdb=" OP1   A E  33 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" O2'   G E  68 "
            pdb=" O4'   A E  69 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" NE2 HIS C 517 "
            pdb=" O2'   A E  77 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" OH  TYR A 885 "
            pdb=" OE1 GLU A1054 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   PHE B 542 "
            pdb=" OG1 THR B 557 "
     model   vdw
     2.227 3.040
  ... (remaining 93993 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:             2.200
  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:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.400
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6650
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      :  0.004   0.046  12702  Z= 0.205
  Angle     :  0.616   8.300  17605  Z= 0.322
  Chirality :  0.038   0.159   2000
  Planarity :  0.004   0.053   1918
  Dihedral  : 19.266 176.079   5446
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  : 22.45 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.24), residues: 1244
  helix:  1.67 (0.23), residues: 536
  sheet: -0.58 (0.55), residues: 98
  loop : -1.35 (0.24), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 696 
 TYR   0.013   0.001   TYR A1199 
 PHE   0.025   0.001   PHE C 532 
 TRP   0.035   0.002   TRP A 725 
 HIS   0.006   0.001   HIS C 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (12694)
  covalent geometry    : angle       0.61623 (17601)
  hydrogen bonds       : bond        0.20577 (  515)
  hydrogen bonds       : angle       6.14154 ( 1421)
  metal coordination   : bond        0.00925 (    8)
  metal coordination   : angle       0.58789 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.298 
Fit side-chains
REVERT: C  570 ARG cc_start: 0.8342 (mtm110) cc_final: 0.7214 (ttp80)
  outliers start: 1
  outliers final: 1
  residues processed: 46
  average time/residue: 0.1007
  time to fit residues: 7.3158
Evaluate side-chains
  47 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 46
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  897 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:   30.0000
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:   20.0000
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:   20.0000
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    7.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 648 ASN
B 649 GLN
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 678 GLN
B 730 HIS
C 521 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.056788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.040016 restraints weight = 83058.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 4.81
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.0949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  12702  Z= 0.241
  Angle     :  0.615   6.412  17605  Z= 0.314
  Chirality :  0.039   0.159   2000
  Planarity :  0.004   0.048   1918
  Dihedral  : 18.799 176.497   2842
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 20.93 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.24), residues: 1244
  helix:  1.48 (0.22), residues: 571
  sheet: -0.49 (0.54), residues: 99
  loop : -1.33 (0.25), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1208 
 TYR   0.014   0.001   TYR B 698 
 PHE   0.012   0.001   PHE B 598 
 TRP   0.017   0.002   TRP A 725 
 HIS   0.005   0.001   HIS B 685 

Details of bonding type rmsd
  covalent geometry    : bond        0.00542 (12694)
  covalent geometry    : angle       0.61468 (17601)
  hydrogen bonds       : bond        0.06786 (  515)
  hydrogen bonds       : angle       4.54651 ( 1421)
  metal coordination   : bond        0.01132 (    8)
  metal coordination   : angle       1.25377 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 46
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A 1322 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.7502 (mpp)
  outliers start: 35
  outliers final: 11
  residues processed: 77
  average time/residue: 0.0827
  time to fit residues: 10.3317
Evaluate side-chains
  58 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 THR
Chi-restraints excluded: chain A residue 1322 MET
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  600 HIS
Chi-restraints excluded: chain B residue  644 VAL
Chi-restraints excluded: chain B residue  742 LEU
Chi-restraints excluded: chain C residue  545 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 126 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 4 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 129 optimal weight:   50.0000
   chunk 58 optimal weight:    7.9990
   chunk 63 optimal weight:   10.0000
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 567 ASN
** A 933 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.056678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.040122 restraints weight = 84570.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 4.72
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  12702  Z= 0.226
  Angle     :  0.594   6.837  17605  Z= 0.301
  Chirality :  0.039   0.163   2000
  Planarity :  0.004   0.050   1918
  Dihedral  : 18.772 176.701   2839
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 21.11 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.24), residues: 1244
  helix:  1.53 (0.22), residues: 573
  sheet: -0.55 (0.53), residues: 101
  loop : -1.39 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 570 
 TYR   0.011   0.001   TYR B 698 
 PHE   0.009   0.001   PHE A1148 
 TRP   0.021   0.002   TRP A 725 
 HIS   0.005   0.001   HIS C 517 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (12694)
  covalent geometry    : angle       0.59343 (17601)
  hydrogen bonds       : bond        0.06347 (  515)
  hydrogen bonds       : angle       4.28230 ( 1421)
  metal coordination   : bond        0.00919 (    8)
  metal coordination   : angle       1.35410 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 47
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A  425 ASP cc_start: 0.8363 (OUTLIER) cc_final: 0.8072 (t0)
REVERT: A  602 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7546 (pp20)
REVERT: A  939 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8965 (ttmm)
REVERT: B  697 MET cc_start: 0.8985 (mpp) cc_final: 0.7969 (ptm)
REVERT: B  712 ASP cc_start: 0.9263 (t0) cc_final: 0.8755 (p0)
  outliers start: 33
  outliers final: 18
  residues processed: 78
  average time/residue: 0.0949
  time to fit residues: 11.4243
Evaluate side-chains
  67 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 46
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  602 GLU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  704 LEU
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  939 LYS
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue 1153 ILE
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 THR
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  634 MET
Chi-restraints excluded: chain B residue  644 VAL
Chi-restraints excluded: chain C residue  523 VAL
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  576 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 121 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0030
   chunk 84 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 101 optimal weight:    8.9990
   chunk 111 optimal weight:    0.0870
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.8174

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 933 HIS
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 660 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.057116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.040671 restraints weight = 84148.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 4.66
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.1727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12702  Z= 0.136
  Angle     :  0.513   5.905  17605  Z= 0.261
  Chirality :  0.036   0.164   2000
  Planarity :  0.004   0.047   1918
  Dihedral  : 18.661 175.801   2839
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.65 %
    Favored  : 75.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.27 (0.24), residues: 1244
  helix:  1.71 (0.22), residues: 574
  sheet: -0.58 (0.55), residues: 99
  loop : -1.32 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 746 
 TYR   0.009   0.001   TYR B 698 
 PHE   0.008   0.001   PHE A1148 
 TRP   0.025   0.001   TRP A 725 
 HIS   0.003   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (12694)
  covalent geometry    : angle       0.51234 (17601)
  hydrogen bonds       : bond        0.05051 (  515)
  hydrogen bonds       : angle       3.90012 ( 1421)
  metal coordination   : bond        0.00571 (    8)
  metal coordination   : angle       1.15626 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 46
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  949 MET cc_start: 0.8982 (mmm) cc_final: 0.8633 (mtm)
REVERT: A 1087 GLN cc_start: 0.9488 (OUTLIER) cc_final: 0.9265 (pt0)
REVERT: B  639 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8082 (mm)
REVERT: B  712 ASP cc_start: 0.9285 (t0) cc_final: 0.8779 (p0)
  outliers start: 28
  outliers final: 15
  residues processed: 71
  average time/residue: 0.0911
  time to fit residues: 10.3883
Evaluate side-chains
  62 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 45
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  958 THR
Chi-restraints excluded: chain A residue 1087 GLN
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  644 VAL
Chi-restraints excluded: chain C residue  523 VAL
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  576 LEU
Chi-restraints excluded: chain C residue  735 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 75 optimal weight:    8.9990
   chunk 88 optimal weight:    0.8980
   chunk 122 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   chunk 93 optimal weight:   10.0000
   chunk 100 optimal weight:   30.0000
   chunk 81 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.056898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.040524 restraints weight = 85103.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 4.61
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.1847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12702  Z= 0.154
  Angle     :  0.522   6.256  17605  Z= 0.265
  Chirality :  0.036   0.165   2000
  Planarity :  0.004   0.075   1918
  Dihedral  : 18.608 175.746   2839
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.47 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.24), residues: 1244
  helix:  1.78 (0.22), residues: 575
  sheet: -0.53 (0.54), residues: 99
  loop : -1.36 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 923 
 TYR   0.009   0.001   TYR B 698 
 PHE   0.009   0.001   PHE A1148 
 TRP   0.027   0.001   TRP A 725 
 HIS   0.003   0.001   HIS A 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (12694)
  covalent geometry    : angle       0.52161 (17601)
  hydrogen bonds       : bond        0.05302 (  515)
  hydrogen bonds       : angle       3.85271 ( 1421)
  metal coordination   : bond        0.00579 (    8)
  metal coordination   : angle       1.19206 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 45
  time to evaluate  : 0.451 
Fit side-chains
REVERT: A  425 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8055 (t0)
REVERT: A  949 MET cc_start: 0.8988 (mmm) cc_final: 0.8652 (mtm)
REVERT: A 1087 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.9282 (pt0)
REVERT: B  639 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8160 (mm)
REVERT: B  697 MET cc_start: 0.9003 (mpp) cc_final: 0.7966 (ptm)
REVERT: B  712 ASP cc_start: 0.9253 (t0) cc_final: 0.8732 (p0)
  outliers start: 28
  outliers final: 18
  residues processed: 71
  average time/residue: 0.0827
  time to fit residues: 9.9872
Evaluate side-chains
  66 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 45
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  897 MET
Chi-restraints excluded: chain A residue 1087 GLN
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 THR
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  644 VAL
Chi-restraints excluded: chain C residue  523 VAL
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  576 LEU
Chi-restraints excluded: chain C residue  735 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 109 optimal weight:    9.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    8.9990
   chunk 5 optimal weight:    0.0000
   chunk 125 optimal weight:    8.9990
   chunk 73 optimal weight:    2.9990
   chunk 80 optimal weight:    4.9990
   chunk 61 optimal weight:    6.9990
   chunk 57 optimal weight:    2.9990
   chunk 92 optimal weight:   30.0000
   overall best weight:    2.1992

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 660 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.056777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.040147 restraints weight = 84188.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 4.74
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.2087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12702  Z= 0.154
  Angle     :  0.517   6.448  17605  Z= 0.261
  Chirality :  0.036   0.166   2000
  Planarity :  0.004   0.048   1918
  Dihedral  : 18.577 174.993   2839
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 21.29 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.24), residues: 1244
  helix:  1.76 (0.22), residues: 581
  sheet: -0.41 (0.52), residues: 104
  loop : -1.39 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 570 
 TYR   0.010   0.001   TYR B 698 
 PHE   0.009   0.001   PHE A1148 
 TRP   0.028   0.001   TRP A 725 
 HIS   0.003   0.001   HIS A 630 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (12694)
  covalent geometry    : angle       0.51658 (17601)
  hydrogen bonds       : bond        0.05207 (  515)
  hydrogen bonds       : angle       3.77032 ( 1421)
  metal coordination   : bond        0.00604 (    8)
  metal coordination   : angle       1.27440 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 45
  time to evaluate  : 0.457 
Fit side-chains
REVERT: A  425 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8063 (t0)
REVERT: A  602 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7410 (pp20)
REVERT: A  949 MET cc_start: 0.8984 (mmm) cc_final: 0.8634 (mtm)
REVERT: A 1087 GLN cc_start: 0.9495 (OUTLIER) cc_final: 0.9274 (pt0)
REVERT: B  600 HIS cc_start: 0.8787 (t70) cc_final: 0.8466 (m170)
REVERT: B  639 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8235 (mm)
REVERT: B  697 MET cc_start: 0.9004 (mpp) cc_final: 0.7981 (ptm)
REVERT: B  712 ASP cc_start: 0.9298 (t0) cc_final: 0.8807 (p0)
  outliers start: 30
  outliers final: 22
  residues processed: 73
  average time/residue: 0.0839
  time to fit residues: 9.9798
Evaluate side-chains
  71 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 45
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  602 GLU
Chi-restraints excluded: chain A residue  632 ILE
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  897 MET
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1038 HIS
Chi-restraints excluded: chain A residue 1087 GLN
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 THR
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  644 VAL
Chi-restraints excluded: chain B residue  660 HIS
Chi-restraints excluded: chain C residue  523 VAL
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  576 LEU
Chi-restraints excluded: chain C residue  735 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 84 optimal weight:    4.9990
   chunk 102 optimal weight:    8.9990
   chunk 41 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0980
   chunk 91 optimal weight:    0.0970
   chunk 29 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 126 optimal weight:    7.9990
   chunk 75 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   overall best weight:    1.4182

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 763 ASN
A1294 HIS
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 660 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.057035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.040534 restraints weight = 83973.949|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 4.63
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12702  Z= 0.117
  Angle     :  0.501   6.771  17605  Z= 0.253
  Chirality :  0.036   0.166   2000
  Planarity :  0.004   0.047   1918
  Dihedral  : 18.546 174.369   2839
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.74 %
    Favored  : 75.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.39 (0.24), residues: 1244
  helix:  1.83 (0.22), residues: 581
  sheet: -0.34 (0.52), residues: 104
  loop : -1.38 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 570 
 TYR   0.010   0.001   TYR A 784 
 PHE   0.009   0.001   PHE A1148 
 TRP   0.029   0.001   TRP A 725 
 HIS   0.012   0.001   HIS B 660 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (12694)
  covalent geometry    : angle       0.50084 (17601)
  hydrogen bonds       : bond        0.04833 (  515)
  hydrogen bonds       : angle       3.66084 ( 1421)
  metal coordination   : bond        0.00425 (    8)
  metal coordination   : angle       1.24164 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 46
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A  425 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8028 (t0)
REVERT: A  602 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7433 (pp20)
REVERT: A  939 LYS cc_start: 0.9297 (OUTLIER) cc_final: 0.8880 (ttmm)
REVERT: A  949 MET cc_start: 0.8973 (mmm) cc_final: 0.8608 (mtm)
REVERT: A 1087 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.9275 (pt0)
REVERT: B  600 HIS cc_start: 0.8753 (t70) cc_final: 0.8454 (m170)
REVERT: B  639 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8185 (mm)
REVERT: B  697 MET cc_start: 0.9002 (mpp) cc_final: 0.7980 (ptm)
REVERT: B  712 ASP cc_start: 0.9284 (t0) cc_final: 0.8780 (p0)
  outliers start: 28
  outliers final: 18
  residues processed: 72
  average time/residue: 0.0818
  time to fit residues: 9.6509
Evaluate side-chains
  68 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 45
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  602 GLU
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  897 MET
Chi-restraints excluded: chain A residue  939 LYS
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1038 HIS
Chi-restraints excluded: chain A residue 1087 GLN
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 THR
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  644 VAL
Chi-restraints excluded: chain C residue  523 VAL
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  576 LEU
Chi-restraints excluded: chain C residue  735 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 111 optimal weight:   40.0000
   chunk 31 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 115 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.056768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.040753 restraints weight = 84866.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3134 rms_B_bonded: 4.47
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start:          0.2297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  12702  Z= 0.155
  Angle     :  0.520   6.839  17605  Z= 0.262
  Chirality :  0.036   0.166   2000
  Planarity :  0.004   0.048   1918
  Dihedral  : 18.513 173.690   2839
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 22.00 %
    Favored  : 75.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.24), residues: 1244
  helix:  1.84 (0.22), residues: 582
  sheet: -0.34 (0.52), residues: 104
  loop : -1.41 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 570 
 TYR   0.012   0.001   TYR A 784 
 PHE   0.008   0.001   PHE A1148 
 TRP   0.030   0.001   TRP A 725 
 HIS   0.003   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (12694)
  covalent geometry    : angle       0.51935 (17601)
  hydrogen bonds       : bond        0.05247 (  515)
  hydrogen bonds       : angle       3.73097 ( 1421)
  metal coordination   : bond        0.00565 (    8)
  metal coordination   : angle       1.34145 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 47
  time to evaluate  : 0.574 
Fit side-chains
REVERT: A  425 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.7989 (t0)
REVERT: A  602 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7430 (pp20)
REVERT: A  939 LYS cc_start: 0.9320 (OUTLIER) cc_final: 0.8913 (ttmm)
REVERT: A  949 MET cc_start: 0.9011 (mmm) cc_final: 0.8680 (mtm)
REVERT: A 1087 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.9282 (pt0)
REVERT: B  600 HIS cc_start: 0.8774 (t70) cc_final: 0.8479 (m170)
REVERT: B  639 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8198 (mm)
REVERT: B  697 MET cc_start: 0.9015 (mpp) cc_final: 0.8093 (ptm)
REVERT: B  712 ASP cc_start: 0.9251 (t0) cc_final: 0.8730 (p0)
  outliers start: 28
  outliers final: 20
  residues processed: 74
  average time/residue: 0.0835
  time to fit residues: 10.2440
Evaluate side-chains
  72 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 47
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  602 GLU
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  897 MET
Chi-restraints excluded: chain A residue  939 LYS
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1087 GLN
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 THR
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  644 VAL
Chi-restraints excluded: chain C residue  523 VAL
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  576 LEU
Chi-restraints excluded: chain C residue  735 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 89 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 93 optimal weight:   10.0000
   chunk 129 optimal weight:   50.0000
   chunk 29 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 101 optimal weight:    0.0970
   chunk 59 optimal weight:    3.9990
   chunk 100 optimal weight:   20.0000
   chunk 28 optimal weight:    0.6980
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.056759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.040204 restraints weight = 84968.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 4.73
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12702  Z= 0.149
  Angle     :  0.517   7.082  17605  Z= 0.258
  Chirality :  0.036   0.166   2000
  Planarity :  0.004   0.048   1918
  Dihedral  : 18.485 172.801   2839
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 22.09 %
    Favored  : 75.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.24), residues: 1244
  helix:  1.87 (0.22), residues: 582
  sheet: -0.16 (0.52), residues: 106
  loop : -1.42 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 570 
 TYR   0.009   0.001   TYR B 698 
 PHE   0.009   0.001   PHE A1148 
 TRP   0.029   0.001   TRP A 725 
 HIS   0.003   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (12694)
  covalent geometry    : angle       0.51646 (17601)
  hydrogen bonds       : bond        0.05077 (  515)
  hydrogen bonds       : angle       3.66907 ( 1421)
  metal coordination   : bond        0.00535 (    8)
  metal coordination   : angle       1.40132 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 48
  time to evaluate  : 0.376 
Fit side-chains
REVERT: A  425 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.8005 (t0)
REVERT: A  602 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7440 (pp20)
REVERT: A  939 LYS cc_start: 0.9286 (OUTLIER) cc_final: 0.8892 (ttmm)
REVERT: A  949 MET cc_start: 0.9000 (mmm) cc_final: 0.8647 (mtm)
REVERT: A 1087 GLN cc_start: 0.9502 (OUTLIER) cc_final: 0.9283 (pt0)
REVERT: B  600 HIS cc_start: 0.8834 (t70) cc_final: 0.8548 (m170)
REVERT: B  639 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8110 (mm)
REVERT: B  697 MET cc_start: 0.9018 (mpp) cc_final: 0.8140 (ptm)
REVERT: B  712 ASP cc_start: 0.9274 (t0) cc_final: 0.8773 (p0)
  outliers start: 29
  outliers final: 20
  residues processed: 75
  average time/residue: 0.0838
  time to fit residues: 10.4756
Evaluate side-chains
  73 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 48
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  602 GLU
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  897 MET
Chi-restraints excluded: chain A residue  939 LYS
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1087 GLN
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 THR
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  644 VAL
Chi-restraints excluded: chain C residue  523 VAL
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  576 LEU
Chi-restraints excluded: chain C residue  735 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 4 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 101 optimal weight:    6.9990
   chunk 75 optimal weight:    7.9990
   chunk 102 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   chunk 1 optimal weight:    0.6980
   chunk 67 optimal weight:    0.5980
   chunk 23 optimal weight:    2.9990
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 687 HIS
** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.056660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.040637 restraints weight = 84814.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 4.48
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12702  Z= 0.158
  Angle     :  0.529   8.268  17605  Z= 0.263
  Chirality :  0.036   0.166   2000
  Planarity :  0.004   0.048   1918
  Dihedral  : 18.463 172.698   2839
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 22.36 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.25), residues: 1244
  helix:  1.87 (0.22), residues: 582
  sheet: -0.09 (0.53), residues: 104
  loop : -1.40 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 570 
 TYR   0.011   0.001   TYR B 698 
 PHE   0.008   0.001   PHE A1148 
 TRP   0.030   0.002   TRP A 725 
 HIS   0.003   0.001   HIS B 632 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (12694)
  covalent geometry    : angle       0.52837 (17601)
  hydrogen bonds       : bond        0.05280 (  515)
  hydrogen bonds       : angle       3.68116 ( 1421)
  metal coordination   : bond        0.00649 (    8)
  metal coordination   : angle       1.33880 (    4)

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

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

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2488 Ramachandran restraints generated.
    1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 48
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  425 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7984 (t0)
REVERT: A  602 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7489 (pp20)
REVERT: A  635 MET cc_start: 0.8053 (tmm) cc_final: 0.7725 (tmm)
REVERT: A  939 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8915 (ttmm)
REVERT: A  949 MET cc_start: 0.9019 (mmm) cc_final: 0.8683 (mtm)
REVERT: A 1087 GLN cc_start: 0.9497 (OUTLIER) cc_final: 0.9285 (pt0)
REVERT: B  600 HIS cc_start: 0.8838 (t70) cc_final: 0.8548 (m170)
REVERT: B  639 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8208 (mm)
REVERT: B  697 MET cc_start: 0.9013 (mpp) cc_final: 0.8083 (ptm)
REVERT: B  712 ASP cc_start: 0.9274 (t0) cc_final: 0.8771 (p0)
  outliers start: 27
  outliers final: 19
  residues processed: 73
  average time/residue: 0.0823
  time to fit residues: 10.0071
Evaluate side-chains
  72 residues out of total 1123 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 48
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  433 SER
Chi-restraints excluded: chain A residue  536 CYS
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  602 GLU
Chi-restraints excluded: chain A residue  659 LEU
Chi-restraints excluded: chain A residue  725 TRP
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  897 MET
Chi-restraints excluded: chain A residue  939 LYS
Chi-restraints excluded: chain A residue  948 ILE
Chi-restraints excluded: chain A residue 1087 GLN
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1237 VAL
Chi-restraints excluded: chain A residue 1239 THR
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  546 VAL
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  639 ILE
Chi-restraints excluded: chain B residue  644 VAL
Chi-restraints excluded: chain C residue  523 VAL
Chi-restraints excluded: chain C residue  545 SER
Chi-restraints excluded: chain C residue  576 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 121 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   chunk 129 optimal weight:   50.0000
   chunk 31 optimal weight:    0.3980
   chunk 104 optimal weight:   10.0000
   chunk 76 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   chunk 113 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 109 optimal weight:   20.0000
   chunk 52 optimal weight:    3.9990
   overall best weight:    3.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A 514 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 728 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.056129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.039946 restraints weight = 84771.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 4.39
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  12702  Z= 0.238
  Angle     :  0.589   8.051  17605  Z= 0.294
  Chirality :  0.038   0.164   2000
  Planarity :  0.004   0.051   1918
  Dihedral  : 18.559 172.626   2839
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 22.45 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.25), residues: 1244
  helix:  1.76 (0.22), residues: 580
  sheet: -0.17 (0.53), residues: 104
  loop : -1.49 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 836 
 TYR   0.012   0.002   TYR B 698 
 PHE   0.011   0.001   PHE A1163 
 TRP   0.031   0.002   TRP A 725 
 HIS   0.005   0.001   HIS A1238 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 (12694)
  covalent geometry    : angle       0.58886 (17601)
  hydrogen bonds       : bond        0.06236 (  515)
  hydrogen bonds       : angle       3.92601 ( 1421)
  metal coordination   : bond        0.01078 (    8)
  metal coordination   : angle       1.15450 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2571.05 seconds
wall clock time: 44 minutes 57.59 seconds (2697.59 seconds total)