Starting phenix.real_space_refine
on Wed Sep 17 22:05:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9asm_43819/09_2025/9asm_43819.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9asm_43819/09_2025/9asm_43819.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9asm_43819/09_2025/9asm_43819.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9asm_43819/09_2025/9asm_43819.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9asm_43819/09_2025/9asm_43819.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9asm_43819/09_2025/9asm_43819.cif"
  }
  resolution = 2.8
  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=  -0.000 sd=   0.011
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      95      5.49       5
     S      61      5.16       5
     C    7017      2.51       5
     N    2052      2.21       5
     O    2419      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: 11648
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 7499
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 916, 7499
          Classifications: {'peptide': 916}
          Link IDs: {'PTRANS': 52, 'TRANS': 863}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 240, 1921
          Classifications: {'peptide': 240}
          Link IDs: {'PTRANS': 10, 'TRANS': 229}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 203
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 203
          Classifications: {'peptide': 24}
          Link IDs: {'PTRANS': 1, 'TRANS': 22}
    Chain: "E"
      Number of atoms: 2019
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 2019
          Classifications: {'RNA': 95}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 42, 'rna3p_pyr': 40}
          Link IDs: {'rna2p': 12, 'rna3p': 82}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' CA': 2, ' ZN': 2}
          Classifications: {'undetermined': 4, 'water': 1}
          Link IDs: {None: 4}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    943  SG  CYS A 561      44.408  20.542 145.715  1.00172.12           S
  ATOM   1901  SG  CYS A 676      41.093  22.263 145.277  1.00178.36           S
  ATOM    751  SG  CYS A 536      24.267  38.767 130.972  1.00181.72           S
  ATOM    766  SG  CYS A 538      24.235  40.054 127.365  1.00190.39           S

  Time building chain proxies: 3.01, per 1000 atoms: 0.26
  Number of scatterers: 11648
  At special positions: 0
  Unit cell: (87.312, 101.008, 193.456, 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      61     16.00
     P      95     15.00
     O    2419      8.00
     N    2052      7.00
     C    7017      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: 1.01
  Conformation dependent library (CDL) restraints added in 513.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  
  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


  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2242

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 8 sheets defined
      55.5% alpha, 12.4% beta
      34 base pairs and 54 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 438 through 453
      removed outlier: 3.549A  pdb=" N   ARG A 442 " --> pdb=" O   THR A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 463
      removed outlier: 3.763A  pdb=" N   ARG A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 512
    Processing helix  chain 'A' and resid 541 through 545
      removed outlier: 3.564A  pdb=" N   THR A 545 " --> pdb=" O   ALA A 542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 656
      removed outlier: 3.615A  pdb=" N   ILE A 656 " --> pdb=" O   LEU A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 709
      removed outlier: 3.513A  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: 3.634A  pdb=" N   CYS A 737 " --> pdb=" O   TYR A 733 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 786
      removed outlier: 6.538A  pdb=" N   TYR A 784 " --> pdb=" O   GLN A 781 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ALA A 785 " --> pdb=" O   LEU A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 807
      removed outlier: 3.572A  pdb=" N   ASN A 806 " --> pdb=" O   HIS A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 830
      removed outlier: 3.896A  pdb=" N   LYS A 815 " --> pdb=" O   LYS A 811 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLN A 816 " --> pdb=" O   GLN A 812 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS A 817 " --> pdb=" O   THR A 813 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 861
      removed outlier: 3.824A  pdb=" N   CYS A 857 " --> pdb=" O   ARG A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 884
      removed outlier: 3.719A  pdb=" N   LEU A 866 " --> pdb=" O   MET A 862 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   MET A 877 " --> pdb=" O   HIS A 873 " (cutoff:3.500A)
      removed outlier: 5.124A  pdb=" N   HIS A 878 " --> pdb=" O   GLN A 874 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   LEU A 879 " --> pdb=" O   CYS A 875 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 897
      removed outlier: 3.585A  pdb=" N   LEU A 893 " --> pdb=" O   ASP A 889 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   MET A 897 " --> pdb=" O   LEU A 893 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 920
    Processing helix  chain 'A' and resid 929 through 933
      removed outlier: 3.547A  pdb=" N   VAL A 932 " --> pdb=" O   ASP A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 941 through 950
    Processing helix  chain 'A' and resid 965 through 988
      removed outlier: 3.670A  pdb=" N   PHE A 970 " --> pdb=" O   GLU A 966 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A 971 " --> pdb=" O   ARG A 967 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ALA A 974 " --> pdb=" O   PHE A 970 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 992 through 1004
    Processing helix  chain 'A' and resid 1005 through 1017
      removed outlier: 3.836A  pdb=" N   LYS A1015 " --> pdb=" O   MET A1011 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU A1016 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1018 through 1021
    Processing helix  chain 'A' and resid 1027 through 1031
      removed outlier: 4.257A  pdb=" N   LEU A1030 " --> pdb=" O   GLY A1027 " (cutoff:3.500A)
      removed outlier: 3.928A  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: 3.566A  pdb=" N   ALA A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE A1069 " --> pdb=" O   GLY A1065 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1080
    Processing helix  chain 'A' and resid 1084 through 1090
      removed outlier: 3.828A  pdb=" N   GLU A1090 " --> pdb=" O   LEU A1086 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1098
      removed outlier: 3.627A  pdb=" N   ILE A1098 " --> pdb=" O   ARG A1095 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1101 through 1115
      removed outlier: 3.727A  pdb=" N   GLN A1105 " --> pdb=" O   SER A1101 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLU A1109 " --> pdb=" O   GLN A1105 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   PHE A1110 " --> pdb=" O   LYS A1106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1128
      removed outlier: 4.133A  pdb=" N   LEU A1124 " --> pdb=" O   HIS A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1166
      removed outlier: 3.986A  pdb=" N   SER A1152 " --> pdb=" O   PHE A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1182
    Processing helix  chain 'A' and resid 1183 through 1194
    Processing helix  chain 'A' and resid 1195 through 1199
      removed outlier: 3.915A  pdb=" N   GLU A1198 " --> pdb=" O   GLY A1195 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   TYR A1199 " --> pdb=" O   MET A1196 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1195 through 1199'
    Processing helix  chain 'A' and resid 1203 through 1208
      removed outlier: 4.170A  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: 4.114A  pdb=" N   VAL A1237 " --> pdb=" O   ASP A1233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1256
      removed outlier: 3.671A  pdb=" N   PHE A1252 " --> pdb=" O   ARG A1248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1271
    Processing helix  chain 'A' and resid 1316 through 1332
    Processing helix  chain 'A' and resid 1334 through 1348
      removed outlier: 3.585A  pdb=" N   ALA A1338 " --> pdb=" O   PHE A1334 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LYS A1347 " --> pdb=" O   PHE A1343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1348 through 1360
      removed outlier: 3.834A  pdb=" N   LEU A1352 " --> pdb=" O   TYR A1348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 511 through 524
    Processing helix  chain 'B' and resid 560 through 577
    Processing helix  chain 'B' and resid 591 through 601
    Processing helix  chain 'B' and resid 607 through 616
    Processing helix  chain 'B' and resid 619 through 631
      removed outlier: 3.608A  pdb=" N   ASN B 631 " --> pdb=" O   CYS B 627 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 685
      removed outlier: 3.710A  pdb=" N   GLN B 674 " --> pdb=" O   ARG B 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 702
      removed outlier: 4.286A  pdb=" N   LEU B 694 " --> pdb=" O   ASN B 690 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 718
      removed outlier: 3.694A  pdb=" N   LEU B 718 " --> pdb=" O   SER B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 749
      removed outlier: 3.657A  pdb=" N   LEU B 732 " --> pdb=" O   ASN B 728 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 728 through 749
      removed outlier: 3.833A  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: 6.652A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLY A 603 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   VAL A 686 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 9.418A  pdb=" N   PHE A 688 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
      removed outlier: 9.604A  pdb=" N   TYR A 599 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 413 through 415
      removed outlier: 6.652A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 696 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLY A 603 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   VAL A 686 " --> pdb=" O   PHE A 601 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   PHE A 601 " --> pdb=" O   VAL A 686 " (cutoff:3.500A)
      removed outlier: 9.418A  pdb=" N   PHE A 688 " --> pdb=" O   TYR A 599 " (cutoff:3.500A)
      removed outlier: 9.604A  pdb=" N   TYR A 599 " --> pdb=" O   PHE A 688 " (cutoff:3.500A)
      removed outlier: 11.877A  pdb=" N   GLU A 602 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   VAL A 578 " --> pdb=" O   GLU A 602 " (cutoff:3.500A)
      removed outlier: 4.544A  pdb=" N   PHE A 604 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   CYS A 618 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 711 through 712
      removed outlier: 3.837A  pdb=" N   LYS A 711 " --> pdb=" O   LYS A 849 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 756 through 758
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1283 through 1290
      removed outlier: 6.967A  pdb=" N   THR A1299 " --> pdb=" O   LEU A1287 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   THR A1289 " --> pdb=" O   THR A1297 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   THR A1297 " --> pdb=" O   THR A1289 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   TYR A1298 " --> pdb=" O   LYS A1313 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LYS A1313 " --> pdb=" O   TYR A1298 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   VAL A1300 " --> pdb=" O   CYS A1311 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   CYS A1311 " --> pdb=" O   VAL A1300 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   VAL A1302 " --> pdb=" O   ILE A1309 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 495 through 496
    Processing sheet with id=AA7, first strand: chain 'B' and resid 529 through 534
      removed outlier: 4.124A  pdb=" N   VAL B 529 " --> pdb=" O   THR B 547 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   PHE B 542 " --> pdb=" O   ALA B 558 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE B 548 " --> pdb=" O   THR B 552 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   THR B 552 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 640 through 644

    489 hydrogen bonds defined for protein.
    1410 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      80 hydrogen bonds
      136 hydrogen bond angles
      0 basepair planarities
      34 basepair parallelities
      54 stacking parallelities
  Total time for adding SS restraints: 2.03

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3318
        1.34 -     1.46: 2515
        1.46 -     1.58: 5986
        1.58 -     1.70: 187
        1.70 -     1.81: 97
  Bond restraints: 12103
  Sorted by residual:
  bond pdb=" CB  GLU C 737 "
       pdb=" CG  GLU C 737 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.09e+00
  bond pdb=" CA  MET A 949 "
       pdb=" C   MET A 949 "
    ideal  model  delta    sigma   weight residual
    1.522  1.504  0.018 1.37e-02 5.33e+03 1.79e+00
  bond pdb=" N   MET A 427 "
       pdb=" CA  MET A 427 "
    ideal  model  delta    sigma   weight residual
    1.457  1.473 -0.016 1.29e-02 6.01e+03 1.48e+00
  bond pdb=" CB  GLU C 747 "
       pdb=" CG  GLU C 747 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.23e+00
  bond pdb=" C   GLN A 924 "
       pdb=" O   GLN A 924 "
    ideal  model  delta    sigma   weight residual
    1.238  1.249 -0.011 1.08e-02 8.57e+03 1.11e+00
  ... (remaining 12098 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 16682
        2.49 -     4.99: 103
        4.99 -     7.48: 11
        7.48 -     9.98: 2
        9.98 -    12.47: 1
  Bond angle restraints: 16799
  Sorted by residual:
  angle pdb=" C   PRO A 426 "
        pdb=" N   MET A 427 "
        pdb=" CA  MET A 427 "
      ideal   model   delta    sigma   weight residual
     121.54  130.51   -8.97 1.91e+00 2.74e-01 2.21e+01
  angle pdb=" CA  MET A 427 "
        pdb=" CB  MET A 427 "
        pdb=" CG  MET A 427 "
      ideal   model   delta    sigma   weight residual
     114.10  122.69   -8.59 2.00e+00 2.50e-01 1.84e+01
  angle pdb=" CB  MET A 427 "
        pdb=" CG  MET A 427 "
        pdb=" SD  MET A 427 "
      ideal   model   delta    sigma   weight residual
     112.70  125.17  -12.47 3.00e+00 1.11e-01 1.73e+01
  angle pdb=" CA  GLU C 737 "
        pdb=" CB  GLU C 737 "
        pdb=" CG  GLU C 737 "
      ideal   model   delta    sigma   weight residual
     114.10  121.38   -7.28 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" CA  GLU C 744 "
        pdb=" CB  GLU C 744 "
        pdb=" CG  GLU C 744 "
      ideal   model   delta    sigma   weight residual
     114.10  120.92   -6.82 2.00e+00 2.50e-01 1.16e+01
  ... (remaining 16794 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.78: 7121
       35.78 -    71.56: 310
       71.56 -   107.33: 32
      107.33 -   143.11: 1
      143.11 -   178.89: 2
  Dihedral angle restraints: 7466
    sinusoidal: 4008
      harmonic: 3458
  Sorted by residual:
  dihedral pdb=" O4'   U E  84 "
           pdb=" C1'   U E  84 "
           pdb=" N1    U E  84 "
           pdb=" C2    U E  84 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   65.46  134.54     1      1.50e+01 4.44e-03 7.26e+01
  dihedral pdb=" O4'   C E  15 "
           pdb=" C1'   C E  15 "
           pdb=" N1    C E  15 "
           pdb=" C2    C E  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.11  178.89     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   C E 124 "
           pdb=" C1'   C E 124 "
           pdb=" N1    C E 124 "
           pdb=" C2    C E 124 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   45.17 -173.17     1      1.70e+01 3.46e-03 6.62e+01
  ... (remaining 7463 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1353
       0.029 -    0.059: 357
       0.059 -    0.088: 102
       0.088 -    0.118: 76
       0.118 -    0.147: 14
  Chirality restraints: 1902
  Sorted by residual:
  chirality pdb=" CB  ILE A 508 "
            pdb=" CA  ILE A 508 "
            pdb=" CG1 ILE A 508 "
            pdb=" CG2 ILE A 508 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.43e-01
  chirality pdb=" CA  MET A 427 "
            pdb=" N   MET A 427 "
            pdb=" C   MET A 427 "
            pdb=" CB  MET A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" C1'   U E  84 "
            pdb=" O4'   U E  84 "
            pdb=" C2'   U E  84 "
            pdb=" N1    U E  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.33    0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 1899 not shown)

  Planarity restraints: 1820
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 748 "    0.010 2.00e-02 2.50e+03   2.01e-02 4.03e+00
        pdb=" CD  GLU C 748 "   -0.035 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 748 "    0.013 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 748 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 597 "   -0.016 2.00e-02 2.50e+03   1.26e-02 3.16e+00
        pdb=" CG  TYR B 597 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 597 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 597 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 597 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 597 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 597 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 597 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A E  13 "   -0.019 2.00e-02 2.50e+03   9.86e-03 2.67e+00
        pdb=" N9    A E  13 "    0.026 2.00e-02 2.50e+03
        pdb=" C8    A E  13 "    0.000 2.00e-02 2.50e+03
        pdb=" N7    A E  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A E  13 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A E  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6    A E  13 "   -0.004 2.00e-02 2.50e+03
        pdb=" N1    A E  13 "   -0.002 2.00e-02 2.50e+03
        pdb=" C2    A E  13 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A E  13 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    A E  13 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1817 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 2973
        2.81 -     3.33: 10056
        3.33 -     3.85: 19154
        3.85 -     4.38: 22262
        4.38 -     4.90: 36273
  Nonbonded interactions: 90718
  Sorted by model distance:
  nonbonded pdb=" O2'   G E  55 "
            pdb=" O4'   G E  56 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" O2'   U E  23 "
            pdb=" OP1   U E  25 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   LYS C 726 "
            pdb=" NZ  LYS C 726 "
     model   vdw
     2.337 3.120
  nonbonded pdb=" N   ASP A1260 "
            pdb=" OD1 ASP A1260 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" NH2 ARG B 522 "
            pdb=" O5'   A E  47 "
     model   vdw
     2.346 3.120
  ... (remaining 90713 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:             8.950
  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:          0.290
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.120
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6089
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12111  Z= 0.134
  Angle     :  0.515  12.470  16803  Z= 0.273
  Chirality :  0.036   0.147   1902
  Planarity :  0.004   0.043   1820
  Dihedral  : 17.971 178.888   5224
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.04 %
    Favored  : 83.92 %
  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:  1.39 (0.25), residues: 1168
  helix:  2.25 (0.22), residues: 567
  sheet:  0.46 (0.42), residues: 143
  loop : -0.63 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 961 
 TYR   0.031   0.001   TYR B 597 
 PHE   0.016   0.001   PHE A1148 
 TRP   0.027   0.001   TRP A1357 
 HIS   0.011   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12103)
  covalent geometry    : angle       0.51166 (16799)
  hydrogen bonds       : bond        0.17558 (  562)
  hydrogen bonds       : angle       5.28621 ( 1546)
  metal coordination   : bond        0.01595 (    8)
  metal coordination   : angle       3.97195 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.361 
Fit side-chains
  outliers start: 11
  outliers final: 10
  residues processed: 71
  average time/residue: 0.6177
  time to fit residues: 47.5407
Evaluate side-chains
  69 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  676 CYS
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue 1035 ASP
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1202 THR
Chi-restraints excluded: chain A residue 1302 VAL
Chi-restraints excluded: chain A residue 1309 ILE
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  552 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 123 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A1008 HIS
B 600 HIS
B 648 ASN
** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.078294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.045800 restraints weight = 34217.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 2.77
r_work: 0.2664 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.0883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  12111  Z= 0.246
  Angle     :  0.562   8.126  16803  Z= 0.294
  Chirality :  0.040   0.167   1902
  Planarity :  0.004   0.040   1820
  Dihedral  : 18.447 178.431   2761
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 12.87 %
    Favored  : 85.34 %
  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:  1.35 (0.25), residues: 1168
  helix:  2.17 (0.22), residues: 585
  sheet:  0.33 (0.40), residues: 155
  loop : -0.70 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 961 
 TYR   0.028   0.002   TYR B 597 
 PHE   0.017   0.001   PHE A1148 
 TRP   0.014   0.001   TRP A1357 
 HIS   0.011   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00581 (12103)
  covalent geometry    : angle       0.55544 (16799)
  hydrogen bonds       : bond        0.06991 (  562)
  hydrogen bonds       : angle       4.28009 ( 1546)
  metal coordination   : bond        0.02166 (    8)
  metal coordination   : angle       5.42667 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 58
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  511 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8761 (mtmm)
REVERT: C  747 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8067 (pp20)
  outliers start: 19
  outliers final: 7
  residues processed: 74
  average time/residue: 0.6302
  time to fit residues: 50.4752
Evaluate side-chains
  66 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 LYS
Chi-restraints excluded: chain A residue  676 CYS
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue  935 MET
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1272 LEU
Chi-restraints excluded: chain A residue 1344 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 107 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 29 optimal weight:    0.3980
   chunk 74 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 81 optimal weight:    0.5980
   chunk 122 optimal weight:   40.0000
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
B 600 HIS
** B 649 GLN ** 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 = 0.3695 r_free = 0.3695 target = 0.079135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.046759 restraints weight = 34428.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 2.77
r_work: 0.2689 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.1019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12111  Z= 0.168
  Angle     :  0.503   6.335  16803  Z= 0.264
  Chirality :  0.037   0.150   1902
  Planarity :  0.004   0.040   1820
  Dihedral  : 18.309 178.212   2753
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 13.53 %
    Favored  : 85.05 %
  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:  1.44 (0.25), residues: 1168
  helix:  2.28 (0.22), residues: 585
  sheet:  0.38 (0.41), residues: 156
  loop : -0.71 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 961 
 TYR   0.026   0.001   TYR B 597 
 PHE   0.016   0.001   PHE A1148 
 TRP   0.014   0.001   TRP A1357 
 HIS   0.013   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (12103)
  covalent geometry    : angle       0.49969 (16799)
  hydrogen bonds       : bond        0.05640 (  562)
  hydrogen bonds       : angle       3.95569 ( 1546)
  metal coordination   : bond        0.01664 (    8)
  metal coordination   : angle       3.94075 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A  511 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8784 (mtmm)
  outliers start: 15
  outliers final: 3
  residues processed: 69
  average time/residue: 0.6335
  time to fit residues: 47.4614
Evaluate side-chains
  61 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 LYS
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1289 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 92 optimal weight:    8.9990
   chunk 58 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   chunk 89 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 111 optimal weight:    0.0040
   chunk 56 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
B 600 HIS
B 649 GLN
** B 660 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.080874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.048908 restraints weight = 34520.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.2926 rms_B_bonded: 2.81
r_work: 0.2762 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12111  Z= 0.091
  Angle     :  0.458   7.961  16803  Z= 0.238
  Chirality :  0.035   0.153   1902
  Planarity :  0.004   0.045   1820
  Dihedral  : 18.198 179.531   2750
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 14.95 %
    Favored  : 84.67 %
  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:  1.80 (0.25), residues: 1168
  helix:  2.55 (0.21), residues: 586
  sheet:  0.64 (0.41), residues: 153
  loop : -0.54 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 961 
 TYR   0.027   0.001   TYR B 597 
 PHE   0.011   0.001   PHE A1148 
 TRP   0.013   0.001   TRP A1357 
 HIS   0.014   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00184 (12103)
  covalent geometry    : angle       0.45628 (16799)
  hydrogen bonds       : bond        0.03807 (  562)
  hydrogen bonds       : angle       3.60716 ( 1546)
  metal coordination   : bond        0.01187 (    8)
  metal coordination   : angle       2.52968 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.425 
Fit side-chains
REVERT: A  511 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8792 (mtmm)
REVERT: B  520 MET cc_start: 0.8285 (tmm) cc_final: 0.8060 (tmm)
  outliers start: 4
  outliers final: 0
  residues processed: 60
  average time/residue: 0.6890
  time to fit residues: 44.5362
Evaluate side-chains
  57 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  511 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 76 optimal weight:    7.9990
   chunk 61 optimal weight:    0.6980
   chunk 1 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   chunk 83 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 600 HIS
** B 649 GLN ** 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 = 0.3724 r_free = 0.3724 target = 0.080489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.048542 restraints weight = 34488.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.81
r_work: 0.2745 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1407

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12111  Z= 0.101
  Angle     :  0.459   7.140  16803  Z= 0.238
  Chirality :  0.035   0.157   1902
  Planarity :  0.003   0.041   1820
  Dihedral  : 18.095 179.848   2748
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.57 %
    Favored  : 84.20 %
  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:  1.97 (0.25), residues: 1168
  helix:  2.70 (0.22), residues: 586
  sheet:  0.71 (0.41), residues: 153
  loop : -0.48 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 961 
 TYR   0.028   0.001   TYR B 597 
 PHE   0.012   0.001   PHE A1148 
 TRP   0.014   0.001   TRP A1357 
 HIS   0.012   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (12103)
  covalent geometry    : angle       0.45706 (16799)
  hydrogen bonds       : bond        0.04088 (  562)
  hydrogen bonds       : angle       3.53536 ( 1546)
  metal coordination   : bond        0.01405 (    8)
  metal coordination   : angle       2.92395 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.418 
Fit side-chains
REVERT: B  520 MET cc_start: 0.8338 (tmm) cc_final: 0.8074 (tmm)
  outliers start: 13
  outliers final: 4
  residues processed: 69
  average time/residue: 0.6127
  time to fit residues: 45.9495
Evaluate side-chains
  61 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  565 THR
Chi-restraints excluded: chain A residue 1289 THR
Chi-restraints excluded: chain B residue  547 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 125 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 56 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 649 GLN ** 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 = 0.3693 r_free = 0.3693 target = 0.079215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.046673 restraints weight = 34503.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.82
r_work: 0.2681 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12111  Z= 0.163
  Angle     :  0.502   9.517  16803  Z= 0.260
  Chirality :  0.037   0.158   1902
  Planarity :  0.004   0.042   1820
  Dihedral  : 18.095 179.800   2748
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.23 %
    Favored  : 83.73 %
  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:  1.84 (0.25), residues: 1168
  helix:  2.63 (0.22), residues: 586
  sheet:  0.56 (0.40), residues: 156
  loop : -0.56 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 961 
 TYR   0.030   0.001   TYR B 597 
 PHE   0.016   0.001   PHE A1148 
 TRP   0.014   0.001   TRP A1357 
 HIS   0.012   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (12103)
  covalent geometry    : angle       0.49842 (16799)
  hydrogen bonds       : bond        0.05329 (  562)
  hydrogen bonds       : angle       3.72096 ( 1546)
  metal coordination   : bond        0.01856 (    8)
  metal coordination   : angle       4.09361 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.448 
Fit side-chains
  outliers start: 11
  outliers final: 4
  residues processed: 69
  average time/residue: 0.6268
  time to fit residues: 47.1062
Evaluate side-chains
  62 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  565 THR
Chi-restraints excluded: chain A residue 1289 THR
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  547 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 96 optimal weight:   10.0000
   chunk 95 optimal weight:    2.9990
   chunk 118 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 76 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 102 optimal weight:    0.0000
   chunk 20 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.1188

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

Flipped N/Q/H residues before XYZ refinement:
** B 649 GLN ** 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 = 0.3709 r_free = 0.3709 target = 0.079723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.047358 restraints weight = 34153.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.2882 rms_B_bonded: 2.79
r_work: 0.2712 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.1431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12111  Z= 0.134
  Angle     :  0.494  11.643  16803  Z= 0.254
  Chirality :  0.036   0.158   1902
  Planarity :  0.004   0.042   1820
  Dihedral  : 18.095 179.831   2748
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.85 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.86 (0.25), residues: 1168
  helix:  2.62 (0.21), residues: 587
  sheet:  0.59 (0.41), residues: 155
  loop : -0.53 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 961 
 TYR   0.031   0.001   TYR B 597 
 PHE   0.014   0.001   PHE A1148 
 TRP   0.015   0.001   TRP A1357 
 HIS   0.013   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (12103)
  covalent geometry    : angle       0.49113 (16799)
  hydrogen bonds       : bond        0.04774 (  562)
  hydrogen bonds       : angle       3.64061 ( 1546)
  metal coordination   : bond        0.01613 (    8)
  metal coordination   : angle       3.53348 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.448 
Fit side-chains
  outliers start: 11
  outliers final: 6
  residues processed: 69
  average time/residue: 0.6587
  time to fit residues: 49.3065
Evaluate side-chains
  64 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  565 THR
Chi-restraints excluded: chain A residue 1048 ILE
Chi-restraints excluded: chain A residue 1114 ILE
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1289 THR
Chi-restraints excluded: chain A residue 1344 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 61 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 118 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 111 optimal weight:    5.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A1170 HIS
** B 600 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 649 GLN ** 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 = 0.3682 r_free = 0.3682 target = 0.078436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.045918 restraints weight = 34287.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 2.76
r_work: 0.2666 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start:          0.1532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12111  Z= 0.203
  Angle     :  0.549  12.129  16803  Z= 0.282
  Chirality :  0.038   0.167   1902
  Planarity :  0.004   0.042   1820
  Dihedral  : 18.114 179.439   2748
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 15.80 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.25), residues: 1168
  helix:  2.53 (0.22), residues: 584
  sheet:  0.51 (0.41), residues: 156
  loop : -0.62 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 961 
 TYR   0.031   0.001   TYR B 597 
 PHE   0.017   0.001   PHE A1148 
 TRP   0.015   0.001   TRP A1357 
 HIS   0.012   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 (12103)
  covalent geometry    : angle       0.54404 (16799)
  hydrogen bonds       : bond        0.06019 (  562)
  hydrogen bonds       : angle       3.86034 ( 1546)
  metal coordination   : bond        0.02122 (    8)
  metal coordination   : angle       4.72084 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.433 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 65
  average time/residue: 0.6427
  time to fit residues: 45.3767
Evaluate side-chains
  63 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  676 CYS
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1289 THR
Chi-restraints excluded: chain A residue 1344 ILE
Chi-restraints excluded: chain B residue  547 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0770
   chunk 2 optimal weight:    0.0970
   chunk 49 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 98 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** B 649 GLN ** 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 = 0.3733 r_free = 0.3733 target = 0.080736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.048661 restraints weight = 34077.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 2.77
r_work: 0.2756 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  12111  Z= 0.101
  Angle     :  0.494  13.106  16803  Z= 0.253
  Chirality :  0.036   0.182   1902
  Planarity :  0.004   0.042   1820
  Dihedral  : 18.027 179.734   2748
  Min Nonbonded Distance : 2.289

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 15.99 %
    Favored  : 83.44 %
  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:  1.94 (0.25), residues: 1168
  helix:  2.68 (0.21), residues: 584
  sheet:  0.72 (0.41), residues: 153
  loop : -0.49 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 961 
 TYR   0.031   0.001   TYR B 597 
 PHE   0.012   0.001   PHE A1148 
 TRP   0.017   0.001   TRP A1357 
 HIS   0.012   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 (12103)
  covalent geometry    : angle       0.49226 (16799)
  hydrogen bonds       : bond        0.03801 (  562)
  hydrogen bonds       : angle       3.52305 ( 1546)
  metal coordination   : bond        0.01225 (    8)
  metal coordination   : angle       2.66468 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 59
  time to evaluate  : 0.431 
Fit side-chains
  outliers start: 6
  outliers final: 4
  residues processed: 65
  average time/residue: 0.6849
  time to fit residues: 48.3150
Evaluate side-chains
  62 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue 1121 VAL
Chi-restraints excluded: chain A residue 1289 THR
Chi-restraints excluded: chain B residue  547 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 36 optimal weight:    0.0070
   chunk 46 optimal weight:    0.0270
   chunk 49 optimal weight:    0.8980
   chunk 125 optimal weight:    3.9990
   chunk 102 optimal weight:    4.9990
   chunk 124 optimal weight:    6.9990
   chunk 7 optimal weight:    0.0970
   chunk 55 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 111 optimal weight:    3.9990
   overall best weight:    0.4054

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

Flipped N/Q/H residues before XYZ refinement:
** B 649 GLN ** 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 = 0.3741 r_free = 0.3741 target = 0.081082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.048955 restraints weight = 34837.305|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 2.86
r_work: 0.2765 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.1922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  12111  Z= 0.091
  Angle     :  0.479  12.526  16803  Z= 0.242
  Chirality :  0.035   0.168   1902
  Planarity :  0.004   0.042   1820
  Dihedral  : 17.866 178.559   2748
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  : 16.27 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.25), residues: 1168
  helix:  2.81 (0.21), residues: 584
  sheet:  0.83 (0.41), residues: 153
  loop : -0.38 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 961 
 TYR   0.032   0.001   TYR B 597 
 PHE   0.010   0.001   PHE A1148 
 TRP   0.020   0.001   TRP A1357 
 HIS   0.012   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 (12103)
  covalent geometry    : angle       0.47710 (16799)
  hydrogen bonds       : bond        0.03511 (  562)
  hydrogen bonds       : angle       3.38056 ( 1546)
  metal coordination   : bond        0.01337 (    8)
  metal coordination   : angle       2.70771 (    4)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.427 
Fit side-chains
REVERT: B  553 TYR cc_start: 0.8288 (t80) cc_final: 0.7741 (t80)
REVERT: C  745 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8177 (tm-30)
  outliers start: 4
  outliers final: 3
  residues processed: 63
  average time/residue: 0.6793
  time to fit residues: 46.2683
Evaluate side-chains
  61 residues out of total 1057 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 58
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  875 CYS
Chi-restraints excluded: chain A residue 1289 THR
Chi-restraints excluded: chain B residue  547 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 117 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0060
   chunk 46 optimal weight:    0.8980
   chunk 92 optimal weight:    6.9990
   chunk 17 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 121 optimal weight:   40.0000
   chunk 96 optimal weight:    0.9990
   chunk 102 optimal weight:    0.4980
   chunk 118 optimal weight:    3.9990
   overall best weight:    0.6800

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

Flipped N/Q/H residues before XYZ refinement:
** B 649 GLN ** 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 = 0.3725 r_free = 0.3725 target = 0.080567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.048366 restraints weight = 34433.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 2.83
r_work: 0.2738 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  12111  Z= 0.104
  Angle     :  0.496  13.920  16803  Z= 0.250
  Chirality :  0.035   0.164   1902
  Planarity :  0.003   0.042   1820
  Dihedral  : 17.850 178.831   2748
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 16.65 %
    Favored  : 83.07 %
  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:  2.11 (0.25), residues: 1168
  helix:  2.81 (0.21), residues: 585
  sheet:  0.77 (0.41), residues: 155
  loop : -0.40 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 961 
 TYR   0.032   0.001   TYR B 597 
 PHE   0.012   0.001   PHE A1148 
 TRP   0.019   0.001   TRP A1357 
 HIS   0.012   0.001   HIS B 600 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 (12103)
  covalent geometry    : angle       0.49429 (16799)
  hydrogen bonds       : bond        0.03999 (  562)
  hydrogen bonds       : angle       3.43115 ( 1546)
  metal coordination   : bond        0.01362 (    8)
  metal coordination   : angle       2.93440 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4344.12 seconds
wall clock time: 74 minutes 42.03 seconds (4482.03 seconds total)